From a1cc43714d5060ee5505107bfa36398e4bcd613e Mon Sep 17 00:00:00 2001 From: Parrish Payne Date: Fri, 1 Sep 2023 10:51:50 -0500 Subject: [PATCH 1/6] Fix Protocol Titles in Readme files --- protocols/0dda91/README.md | 2 +- protocols/0fdc01/README.md | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/protocols/0dda91/README.md b/protocols/0dda91/README.md index 37b9b1767..c7fc92fe3 100644 --- a/protocols/0dda91/README.md +++ b/protocols/0dda91/README.md @@ -1,4 +1,4 @@ -# Protocol Title (should match metadata of .py file) +# 16S Library pooling ### Author [Opentrons](https://opentrons.com/) diff --git a/protocols/0fdc01/README.md b/protocols/0fdc01/README.md index d228c7f9d..7150753f2 100644 --- a/protocols/0fdc01/README.md +++ b/protocols/0fdc01/README.md @@ -1,5 +1,4 @@ -# Protocol Title -PCR Prep +# PCR Prep ### Author [Opentrons](https://opentrons.com/) From 3902b249b62162c61800eb66c141e60291f6b2f1 Mon Sep 17 00:00:00 2001 From: ncdiehl11 Date: Mon, 4 Sep 2023 19:46:59 -0400 Subject: [PATCH 2/6] fix titleg --- protoBuilds/79e9a1-cleanup/README.json | 27 +++++++++++----------- protocols/79e9a1-cleanup/README.md | 32 +++++++++++++------------- 2 files changed, 29 insertions(+), 30 deletions(-) diff --git a/protoBuilds/79e9a1-cleanup/README.json b/protoBuilds/79e9a1-cleanup/README.json index 400b3e6f0..02293e29f 100644 --- a/protoBuilds/79e9a1-cleanup/README.json +++ b/protoBuilds/79e9a1-cleanup/README.json @@ -1,24 +1,23 @@ { "author": "Opentrons", "categories": { - "NGS Library Prep": [ - "Cleanup" - ] + "Cleanup": [], + "NGS Library Prep": [] }, "description": "This protocol is equipped to perform any of 4x cleanups for the Paragon NGS prep protocol.", "internal": "0b83b7", "labware": "\nNEST 0.2 mL 96-Well PCR Plate, Full Skirt\nNEST 12 Well Reservoir 15 mL #360102\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n\n", - "categories": "* NGS Library Prep\n\t* Cleanup\n\n\n", - "description": "This protocol is equipped to perform any of 4x cleanups for the Paragon NGS prep protocol.\n\n\n", - "internal": "0b83b7\n", - "labware": "* [NEST 0.2 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/nest-0-2-ml-96-well-pcr-plate-full-skirt/)\n* [NEST 12 Well Reservoir 15 mL #360102](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/)\n* [Opentrons 96 Filter Tip Rack 200 \u00b5L](https://shop.opentrons.com/opentrons-200ul-filter-tips/)\n* [Opentrons 96 Filter Tip Rack 20 \u00b5L](https://shop.opentrons.com/opentrons-20ul-filter-tips/)\n\n\n", - "modules": "* [Opentrons Temperature Module (GEN2)](https://shop.opentrons.com/temperature-module-gen2/)\n* [Opentrons Magnetic Module (GEN2)](https://shop.opentrons.com/magnetic-module-gen2/)\n\n\n", - "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n\n", - "pipettes": "* [Opentrons P300 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n\n\n", - "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit \"Run\".\n\n\n", - "title": "Paragon Cleanup" + "author": "\n[Opentrons](https://opentrons.com/)\n\n", + "categories": "\n- NGS Library Prep\n - Cleanup\n\n", + "description": "\nThis protocol is equipped to perform any of 4x cleanups for the Paragon NGS prep protocol.\n\n", + "internal": "\n0b83b7\n", + "labware": "\n- [NEST 0.2 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/nest-0-2-ml-96-well-pcr-plate-full-skirt/)\n- [NEST 12 Well Reservoir 15 mL #360102](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/)\n- [Opentrons 96 Filter Tip Rack 200 \u00b5L](https://shop.opentrons.com/opentrons-200ul-filter-tips/)\n- [Opentrons 96 Filter Tip Rack 20 \u00b5L](https://shop.opentrons.com/opentrons-20ul-filter-tips/)\n\n", + "modules": "\n- [Opentrons Temperature Module (GEN2)](https://shop.opentrons.com/temperature-module-gen2/)\n- [Opentrons Magnetic Module (GEN2)](https://shop.opentrons.com/magnetic-module-gen2/)\n\n", + "notes": "\nIf you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/).\n\n", + "pipettes": "\n- [Opentrons P300 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n- [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n\n", + "process": "\n1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit \"Run\".\n\n", + "title": "NGS Cleanup" }, "modules": [ "Opentrons Temperature Module (GEN2)", @@ -27,5 +26,5 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nOpentrons P300 8 Channel Electronic Pipette (GEN2)\nOpentrons P20 8 Channel Electronic Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit \"Run\".\n", - "title": "Paragon Cleanup" + "title": "NGS Cleanup" } \ No newline at end of file diff --git a/protocols/79e9a1-cleanup/README.md b/protocols/79e9a1-cleanup/README.md index 0bc945b2a..8bf9f8313 100644 --- a/protocols/79e9a1-cleanup/README.md +++ b/protocols/79e9a1-cleanup/README.md @@ -1,37 +1,37 @@ -# Paragon Cleanup - +# NGS Cleanup ### Author -[Opentrons](https://opentrons.com/) +[Opentrons](https://opentrons.com/) ## Categories -* NGS Library Prep - * Cleanup +- NGS Library Prep + - Cleanup ## Description -This protocol is equipped to perform any of 4x cleanups for the Paragon NGS prep protocol. +This protocol is equipped to perform any of 4x cleanups for the Paragon NGS prep protocol. ### Modules -* [Opentrons Temperature Module (GEN2)](https://shop.opentrons.com/temperature-module-gen2/) -* [Opentrons Magnetic Module (GEN2)](https://shop.opentrons.com/magnetic-module-gen2/) +- [Opentrons Temperature Module (GEN2)](https://shop.opentrons.com/temperature-module-gen2/) +- [Opentrons Magnetic Module (GEN2)](https://shop.opentrons.com/magnetic-module-gen2/) ### Labware -* [NEST 0.2 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/nest-0-2-ml-96-well-pcr-plate-full-skirt/) -* [NEST 12 Well Reservoir 15 mL #360102](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/) -* [Opentrons 96 Filter Tip Rack 200 µL](https://shop.opentrons.com/opentrons-200ul-filter-tips/) -* [Opentrons 96 Filter Tip Rack 20 µL](https://shop.opentrons.com/opentrons-20ul-filter-tips/) +- [NEST 0.2 mL 96-Well PCR Plate, Full Skirt](https://shop.opentrons.com/nest-0-2-ml-96-well-pcr-plate-full-skirt/) +- [NEST 12 Well Reservoir 15 mL #360102](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/) +- [Opentrons 96 Filter Tip Rack 200 µL](https://shop.opentrons.com/opentrons-200ul-filter-tips/) +- [Opentrons 96 Filter Tip Rack 20 µL](https://shop.opentrons.com/opentrons-20ul-filter-tips/) ### Pipettes -* [Opentrons P300 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) -* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) +- [Opentrons P300 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) +- [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/) ### Process + 1. Input your protocol parameters above. 2. Download your protocol and unzip if needed. 3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed. @@ -40,10 +40,10 @@ This protocol is equipped to perform any of 4x cleanups for the Paragon NGS prep 6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2). 7. Hit "Run". - ### Additional Notes -If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/). +If you have any questions about this protocol, please contact the Protocol Development Team by filling out the [Troubleshooting Survey](https://protocol-troubleshooting.paperform.co/). ###### Internal + 0b83b7 From 6282410b9b32ca028b8f2675535fe8512610b0c6 Mon Sep 17 00:00:00 2001 From: ncdiehl11 Date: Tue, 5 Sep 2023 09:35:58 -0400 Subject: [PATCH 3/6] display buffers only if samples > 0 --- protoBuilds/gsdx/bacgene.ot2.apiv2.py.json | 2 +- protocols/gsdx/bacgene.ot2.apiv2.py | 115 ++++++++++++--------- 2 files changed, 65 insertions(+), 52 deletions(-) diff --git a/protoBuilds/gsdx/bacgene.ot2.apiv2.py.json b/protoBuilds/gsdx/bacgene.ot2.apiv2.py.json index 4e870dfa6..f46f778af 100644 --- a/protoBuilds/gsdx/bacgene.ot2.apiv2.py.json +++ b/protoBuilds/gsdx/bacgene.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nfrom opentrons.types import Point, Mount\n\n\nmetadata = {\n 'protocolName': 'BACGene',\n 'author': 'Nick Diehl 12:\n raise Exception('Combination of listeria and salmonella samples \\\nexceeds plate capacity')\n\n # define locations of lysis buffer reagents\n lysis_buffer_listeria = lysis_rack.rows_by_name()['B'][\n 1::2]\n lysis_buffer_salmonella = lysis_rack.rows_by_name()['D'][\n 1::2]\n enzyme_listeria_1 = lysis_rack.rows_by_name()['B'][\n ::2]\n enzyme_listeria_2 = lysis_rack.rows_by_name()['C']\n enzyme_salmonella = lysis_rack.rows_by_name()['D'][\n ::2]\n positive_control_l = lysis_rack.wells_by_name()['A1']\n positive_control_s = lysis_rack.wells_by_name()['E1']\n\n # define liquids\n try:\n lysis_buffer_l_prepared_liq = ctx.define_liquid(\n name=\"listeria lysis buffer (prepared)\",\n description=\"\",\n display_color=\"#B925FF\",\n )\n lysis_buffer_l_fresh_liq = ctx.define_liquid(\n name=\"listeria lysis buffer (fresh)\",\n description=\"\",\n display_color=\"#E4ABFF\",\n )\n lysis_buffer_s_prepared_liq = ctx.define_liquid(\n name=\"salmonella lysis buffer (prepared)\",\n description=\"\",\n display_color=\"#FFD600\",\n )\n lysis_buffer_s_fresh_liq = ctx.define_liquid(\n name=\"salmonella lysis buffer (fresh)\",\n description=\"\",\n display_color=\"#FFF2AD\",\n )\n enzyme_listeria_1_liq = ctx.define_liquid(\n name=\"listeria enzyme 1\",\n description=\"\",\n display_color=\"#FF9900\",\n )\n enzyme_listeria_2_liq = ctx.define_liquid(\n name=\"listeria enzyme 2\",\n description=\"\",\n display_color=\"#9DFFD8\",\n )\n enzyme_salmonella_liq = ctx.define_liquid(\n name=\"salmonella enzyme\",\n description=\"\",\n display_color=\"#50D5FF\",\n )\n positive_control_l_liq = ctx.define_liquid(\n name=\"listeria postive control\",\n description=\"\",\n display_color=\"#FF80F5\",\n )\n positive_control_s_liq = ctx.define_liquid(\n name=\"salmonella positive control\",\n description=\"\",\n display_color=\"#7EFF42\",\n )\n samples_listeria_liq_sample = ctx.define_liquid(\n name=\"listeria samples\",\n description=\"\",\n display_color=\"#0EFFFB\",\n )\n samples_listeria_liq_lysis = ctx.define_liquid(\n name=\"listeria samples\",\n description=\"\",\n display_color=\"#0756EA\",\n )\n samples_listeria_liq_pcr = ctx.define_liquid(\n name=\"listeria samples\",\n description=\"\",\n display_color=\"#130183\",\n )\n samples_salmonella_liq_sample = ctx.define_liquid(\n name=\"salmonella samples\",\n description=\"\",\n display_color=\"#F6096D\",\n )\n samples_salmonella_liq_lysis = ctx.define_liquid(\n name=\"salmonella samples\",\n description=\"\",\n display_color=\"#FF0000\",\n )\n samples_salmonella_liq_pcr = ctx.define_liquid(\n name=\"salmonella samples\",\n description=\"\",\n display_color=\"#A92F00\",\n )\n except AttributeError:\n pass\n\n samples_single_listeria = sample_plate.wells()[:num_samples_listeria]\n num_cols_offset_samples_listeria = math.ceil(num_samples_listeria/8)\n samples_single_salmonella = sample_plate.wells()[\n num_cols_offset_samples_listeria*8:\n num_cols_offset_samples_listeria*8+num_samples_salmonella]\n lysis_single_listeria = lysis_plate.wells()[:num_samples_listeria]\n lysis_single_salmonella = lysis_plate.wells()[\n num_cols_offset_samples_listeria*8:\n num_cols_offset_samples_listeria*8+num_samples_salmonella]\n pcr_single_listeria = pcr_plate.wells()[:num_samples_listeria]\n pcr_single_salmonella = pcr_plate.wells()[\n num_cols_offset_samples_listeria*8:\n num_cols_offset_samples_listeria*8+num_samples_salmonella]\n\n # load liquids\n try:\n if num_samples_listeria > 0:\n positive_control_l.load_liquid(positive_control_l_liq, volume=10)\n if num_samples_salmonella > 0:\n positive_control_s.load_liquid(positive_control_s_liq, volume=10)\n [well.load_liquid(samples_listeria_liq_sample,\n volume=30/len(samples_single_listeria))\n for well in samples_single_listeria]\n [well.load_liquid(samples_salmonella_liq_sample,\n volume=10/len(samples_single_salmonella))\n for well in samples_single_salmonella]\n [well.load_liquid(samples_listeria_liq_lysis,\n volume=30/len(lysis_single_listeria))\n for well in lysis_single_listeria]\n [well.load_liquid(samples_salmonella_liq_lysis,\n volume=10/len(lysis_single_salmonella))\n for well in lysis_single_salmonella]\n [well.load_liquid(samples_listeria_liq_pcr,\n volume=30/len(pcr_single_listeria))\n for well in pcr_single_listeria]\n [well.load_liquid(samples_salmonella_liq_pcr,\n volume=10/len(pcr_single_salmonella))\n for well in pcr_single_salmonella]\n except AttributeError:\n pass\n\n single_tip_count_map = {m300: 0, m20: 0}\n tip_ref = m300.tip_racks[0].wells()[0]\n default_current = 1\n\n right = True\n\n def drop(pip):\n nonlocal right\n offset = 30 if right else -15\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=offset))\n pip.drop_tip(drop_loc)\n right = not right\n\n def pick_up_single(pip=m300):\n mount = Mount.LEFT if pip.mount == 'left' else Mount.RIGHT\n current_single = 1/8*default_current\n if not ctx.is_simulating():\n # attenuate pickup current\n ctx._hw_manager.hardware._attached_instruments[\n mount].update_config_item(\n 'pick_up_current', current_single)\n pip.pick_up_tip(\n [well\n for col in pip.tip_racks[-1].columns()\n for well in col[::-1]][single_tip_count_map[pip]])\n single_tip_count_map[pip] += 1\n if not ctx.is_simulating():\n # reset pickup current\n ctx._hw_manager.hardware._attached_instruments[\n mount].update_config_item('pick_up_current', default_current)\n\n def slow_withdraw(pip, well, delay_seconds=2.0, y_offset=0):\n pip.default_speed /= 10\n if delay_seconds > 0:\n ctx.delay(delay_seconds)\n pip.move_to(well.top().move(Point(y=y_offset)))\n pip.default_speed *= 10\n\n def wick(pip, well, x_magnitude=0.5, z_offset=3.0):\n radius = well.diameter/2 if well.diameter else well.width/2\n pip.default_speed /= 2\n pip.move_to(well.bottom().move(Point(x=x_magnitude*radius,\n z=z_offset)))\n pip.default_speed *= 2\n\n \"\"\" create lysis buffer with enzyme \"\"\"\n if DO_CREATE_LYSIS_BUFFER:\n\n vol_enzyme = 500.0\n num_trans = math.ceil(vol_enzyme/tip_ref.max_volume)\n vol_per_trans = round(vol_enzyme/num_trans, 1)\n\n if num_samples_listeria_remaining % 48 == 0 or \\\n num_samples_listeria_remaining % 48 == 47:\n num_partial_listeria_buffers = 0\n num_bvs_effective = 0\n else:\n num_partial_listeria_buffers = 1\n if 2*math.ceil(num_samples_listeria_remaining/2) % 48 == 0:\n num_bvs_effective = 48\n else:\n num_bvs_effective = 2*math.ceil(\n num_samples_listeria_remaining/2) % 48\n\n num_additional_listeria_buffers = math.ceil(\n ((num_samples_listeria-1) - num_bvs_effective)/48)\n\n # print(f'partial: {num_partial_listeria_buffers}')\n # print(f'additional: {num_additional_listeria_buffers}')\n\n enzyme_listeria_1_creation = enzyme_listeria_1[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]\n enzyme_listeria_2_creation = enzyme_listeria_2[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]\n lysis_buffer_listeria_creation = lysis_buffer_listeria[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]\n # print(lysis_buffer_listeria_creation)\n\n # load partial liq\n try:\n [well.load_liquid(\n lysis_buffer_l_prepared_liq,\n volume=11000/num_partial_listeria_buffers)\n for well in lysis_buffer_listeria[:num_partial_listeria_buffers]]\n\n # load full liq\n [well.load_liquid(\n lysis_buffer_l_fresh_liq,\n volume=11000/num_additional_listeria_buffers)\n for well in lysis_buffer_listeria[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]]\n [well.load_liquid(\n enzyme_listeria_1_liq,\n volume=500/num_additional_listeria_buffers)\n for well in enzyme_listeria_1[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]]\n [well.load_liquid(\n enzyme_listeria_2_liq,\n volume=500/num_additional_listeria_buffers)\n for well in enzyme_listeria_2[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]]\n except AttributeError:\n pass\n\n # listeria\n for enzyme1, enzyme2, lysis_buff in zip(\n enzyme_listeria_1_creation,\n enzyme_listeria_2_creation,\n lysis_buffer_listeria_creation):\n # enzyme 1\n pick_up_single(m300)\n for _ in range(num_trans):\n m300.aspirate(\n vol_per_trans, enzyme1.bottom().move(\n Point(x=OFFSET_X_TUBERACK, z=1)))\n slow_withdraw(m300, enzyme1)\n m300.move_to(\n lysis_buff.top().move(\n Point(x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA)))\n m300.dispense(\n vol_per_trans,\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=3)))\n m300.blow_out()\n slow_withdraw(\n m300, lysis_buff, y_offset=OFFSET_Y_LYSIS_BUFFER_LISTERIA)\n drop(m300)\n\n # enzyme 2\n pick_up_single(m300)\n for i in range(num_trans):\n m300.aspirate(\n vol_per_trans, enzyme2.bottom().move(\n Point(x=OFFSET_X_TUBERACK, z=1)))\n slow_withdraw(m300, enzyme2)\n m300.move_to(\n lysis_buff.top().move(Point(\n x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA)))\n m300.dispense(\n vol_per_trans,\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=3)))\n if i == num_trans - 1:\n if DO_MIX:\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n m300.mix(\n 10, 200,\n lysis_buff.bottom().move(Point(\n x=OFFSET_X_TUBERACK,\n z=3, y=OFFSET_Y_LYSIS_BUFFER_LISTERIA)))\n m300.flow_rate.aspirate /= 2\n m300.flow_rate.dispense /= 2\n m300.blow_out(\n lysis_buff.bottom().move(Point(\n x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA, z=3)))\n slow_withdraw(\n m300, lysis_buff, y_offset=OFFSET_Y_LYSIS_BUFFER_LISTERIA)\n drop(m300)\n\n # salmonella\n if num_samples_salmonella_remaining % 48 == 0 or \\\n num_samples_salmonella_remaining == 47:\n num_partial_salmonella_buffers = 0\n num_bvs_effective = 0\n else:\n num_partial_salmonella_buffers = 1\n if 2*math.ceil(num_samples_salmonella_remaining/2) % 48 == 0:\n num_bvs_effective = 48\n else:\n num_bvs_effective = 2*math.ceil(\n num_samples_salmonella_remaining/2) % 48\n\n num_additional_salmonella_buffers = math.ceil(\n ((num_samples_salmonella-1) - num_bvs_effective)/48)\n\n enzyme_salmonella_creation = enzyme_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers+num_additional_salmonella_buffers]\n lysis_buffer_salmonella_creation = lysis_buffer_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers+num_additional_salmonella_buffers]\n\n # load partial liq\n try:\n [well.load_liquid(\n lysis_buffer_s_prepared_liq,\n volume=11000/num_partial_salmonella_buffers)\n for well in lysis_buffer_salmonella[\n :num_partial_salmonella_buffers]]\n\n # load full liq\n [well.load_liquid(\n lysis_buffer_s_fresh_liq,\n volume=11000/num_additional_salmonella_buffers)\n for well in lysis_buffer_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers +\n num_additional_salmonella_buffers]]\n [well.load_liquid(\n enzyme_salmonella_liq,\n volume=500/num_additional_salmonella_buffers)\n for well in enzyme_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers +\n num_additional_salmonella_buffers]]\n except AttributeError:\n pass\n\n for enzyme, lysis_buff in zip(enzyme_salmonella_creation,\n lysis_buffer_salmonella_creation):\n # enzyme\n pick_up_single(m300)\n for i in range(num_trans):\n m300.aspirate(vol_per_trans, enzyme.bottom().move(\n Point(x=OFFSET_X_TUBERACK, z=1)))\n slow_withdraw(m300, enzyme)\n m300.move_to(\n lysis_buff.top().move(\n Point(x=OFFSET_X_TUBERACK,\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)))\n m300.dispense(\n vol_per_trans,\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=3)))\n if i == num_trans - 1:\n if DO_MIX:\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n m300.mix(\n 10, 200,\n lysis_buff.bottom().move(Point(\n x=OFFSET_X_TUBERACK,\n z=3, y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)))\n m300.flow_rate.aspirate /= 2\n m300.flow_rate.dispense /= 2\n m300.blow_out(\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=3)))\n slow_withdraw(\n m300, lysis_buff,\n y_offset=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)\n drop(m300)\n\n \"\"\" transfer lysis buffer to lysis plate \"\"\"\n vol_overage = 20\n\n if num_samples_listeria > 0:\n if DO_DISTRIBUTE_LYSIS_BUFFER:\n lysis_buffer_listeria_dests = lysis_plate.wells()[\n :num_samples_listeria-2] + [\n lysis_plate.wells()[num_samples_listeria-1]]\n vol_lysis_buffer_listeria = 70.0\n num_dests_per_asp = int(\n (tip_ref.max_volume-vol_overage)//vol_lysis_buffer_listeria)\n num_asp = math.ceil(\n len(lysis_buffer_listeria_dests)/num_dests_per_asp)\n lysis_buffer_listeria_dest_sets = [\n lysis_buffer_listeria_dests[i*num_dests_per_asp:\n (i+1)*num_dests_per_asp]\n if i < num_asp - 1\n else lysis_buffer_listeria_dests[i*num_dests_per_asp:]\n for i in range(num_asp)]\n pick_up_single(m300)\n m300.aspirate(\n vol_overage,\n lysis_buffer_listeria[0].bottom().move(Point(\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=OFFSET_Z_LYSIS_BUFFER_LISTERIA)))\n num_asp_listeria_remaining = math.ceil(\n (num_samples_listeria_remaining % 48) / 2)\n bump = 24 - num_asp_listeria_remaining \\\n if 24 - num_asp_listeria_remaining != 24 else 0\n for i, d_set in enumerate(lysis_buffer_listeria_dest_sets):\n set_ind = i + bump\n lysis_buff = lysis_buffer_listeria[set_ind//24]\n # m300.blow_out(lysis_buff.top(-1))\n m300.aspirate(\n len(d_set)*vol_lysis_buffer_listeria,\n lysis_buff.bottom().move(Point(\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=OFFSET_Z_LYSIS_BUFFER_LISTERIA)))\n slow_withdraw(\n m300, lysis_buff, y_offset=OFFSET_Y_LYSIS_BUFFER_LISTERIA)\n for d in d_set:\n m300.dispense(vol_lysis_buffer_listeria, d.bottom(2))\n slow_withdraw(m300, d)\n drop(m300)\n\n if num_samples_salmonella > 0:\n if DO_DISTRIBUTE_LYSIS_BUFFER:\n available_wells = [\n well for col in lysis_plate.columns()[num_cols_listeria:]\n for well in col]\n lysis_buffer_salmonella_dests = available_wells[\n :num_samples_salmonella-2] + [\n available_wells[num_samples_salmonella-1]]\n vol_lysis_buffer_salmonella = 90.0 if not salmonella_meat else 50.0\n num_dests_per_asp = 2 # hard-set for now\n num_asp = math.ceil(\n len(lysis_buffer_salmonella_dests)/num_dests_per_asp)\n lysis_buffer_salmonella_dest_sets = [\n lysis_buffer_salmonella_dests[i*num_dests_per_asp:\n (i+1)*num_dests_per_asp]\n if i < num_asp - 1\n else lysis_buffer_salmonella_dests[i*num_dests_per_asp:]\n for i in range(num_asp)]\n pick_up_single(m300)\n m300.aspirate(\n vol_overage,\n lysis_buffer_salmonella[0].bottom().move(\n Point(y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=OFFSET_Z_LYSIS_BUFFER_SALMONELLA)))\n num_asp_salmonella_remaining = math.ceil(\n (num_samples_salmonella_remaining % 48) / 2)\n bump_check = int(48/num_dests_per_asp)\n bump = bump_check - num_asp_salmonella_remaining \\\n if bump_check - num_asp_salmonella_remaining != bump_check \\\n else 0\n for i, d_set in enumerate(lysis_buffer_salmonella_dest_sets):\n set_ind = i + bump\n lysis_buff = lysis_buffer_salmonella[set_ind//bump_check]\n # m300.blow_out(lysis_buff.top(-1))\n # print('salmonella', i, set_ind, lysis_buff, len(d_set))\n # m300.blow_out(lysis_buff.top(-1))\n m300.aspirate(\n len(d_set)*vol_lysis_buffer_salmonella,\n lysis_buff.bottom().move(Point(\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=OFFSET_Z_LYSIS_BUFFER_SALMONELLA)))\n slow_withdraw(m300, lysis_buff,\n y_offset=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)\n for d in d_set:\n m300.dispense(vol_lysis_buffer_salmonella, d.bottom(2))\n slow_withdraw(m300, d)\n drop(m300)\n\n if DO_TRANSFER_SAMPLE_TO_LYSIS:\n \"\"\" transfer listeria \"\"\"\n vol_listeria = 30.0\n num_sample_cols_listeria = math.ceil((num_samples_listeria-2)/8)\n for s, d in zip(sample_plate.rows()[0][:num_sample_cols_listeria],\n lysis_plate.rows()[0][:num_sample_cols_listeria]):\n if sample_rack_type == 'bioplastics':\n asp_loc = s.bottom(2)\n else:\n asp_loc = s.top(-17.36)\n m300.pick_up_tip()\n m300.aspirate(vol_listeria, asp_loc)\n slow_withdraw(m300, s)\n m300.dispense(vol_listeria, d.bottom(2))\n if DO_MIX:\n m300.mix(3, 50, d.bottom(2))\n m300.blow_out(d.bottom(2))\n slow_withdraw(m300, d)\n drop(m300)\n\n \"\"\" transfer salmonella \"\"\"\n [pip, vol_salmonella] = [m20, 10.0] \\\n if not salmonella_meat else [m300, 50.0]\n num_cols_samples_salmonella = math.ceil((num_samples_salmonella-2)/8)\n for s, d in zip(\n sample_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_samples_salmonella],\n lysis_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_samples_salmonella]):\n pip.pick_up_tip()\n if sample_rack_type == 'bioplastics':\n asp_loc = s.bottom(2)\n else:\n asp_loc = s.top(-17.36)\n pip.aspirate(vol_salmonella, asp_loc)\n slow_withdraw(pip, s)\n pip.dispense(vol_salmonella, d.bottom(2))\n if DO_MIX:\n pip.mix(3, 18, d.bottom(2))\n pip.blow_out(d.bottom(2))\n slow_withdraw(pip, d)\n drop(pip)\n\n if DO_SET_TEMP:\n ctx.delay(minutes=20, msg='Incubating for 20 minutes @ 37C.')\n tempdeck.set_temperature(95)\n ctx.delay(minutes=10, msg='Incubating for 10 minutes @ 95C.')\n tempdeck.set_temperature(37)\n\n vol_sample = 5.0\n\n if DO_TRANSFER_SAMPLE_TO_PCR:\n \"\"\" transfer samples to PCR plate \"\"\"\n\n # listeria\n if num_samples_listeria > 0:\n for s, d in zip(lysis_plate.rows()[0][:num_cols_listeria],\n pcr_plate.rows()[0][:num_cols_listeria]):\n m20.pick_up_tip()\n m20.aspirate(5, s.top()) # pre air gap\n m20.aspirate(vol_sample, s)\n slow_withdraw(m20, s)\n m20.dispense(vol_sample, d.bottom(1))\n # if DO_MIX:\n # m20.mix(3, vol_sample*0.8, d.bottom(1))\n m20.dispense(m20.current_volume, d.bottom(1))\n slow_withdraw(m20, d)\n # wick(m20, d)\n drop(m20)\n\n # salmonella\n if num_samples_salmonella > 0:\n for s, d in zip(\n lysis_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_salmonella],\n pcr_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_salmonella]):\n m20.pick_up_tip()\n m20.aspirate(5, s.top()) # pre air gap\n m20.aspirate(vol_sample, s)\n slow_withdraw(m20, s)\n m20.dispense(vol_sample, d.bottom(1))\n # if DO_MIX:\n # m20.mix(3, vol_sample*0.8, d.bottom(1))\n m20.dispense(m20.current_volume, d.bottom(1))\n slow_withdraw(m20, d)\n m20.air_gap(5)\n # wick(m20, d)\n drop(m20)\n\n if DO_TRANSFER_POSITIVE_CONTROL:\n \"\"\" transfer positive controls \"\"\"\n vol_positive_control = vol_sample\n if num_samples_listeria > 0:\n positive_control_l_dest = pcr_plate.wells()[num_samples_listeria-2]\n pick_up_single(m20)\n m20.aspirate(5, positive_control_l_dest.top()) # pre air gap\n m20.aspirate(vol_positive_control, positive_control_l)\n slow_withdraw(m20, positive_control_l)\n m20.dispense(m20.current_volume, positive_control_l_dest.bottom(1))\n slow_withdraw(m20, positive_control_l_dest)\n # if DO_MIX:\n # m20.mix(3, vol_positive_control*0.8,\n # positive_control_l_dest.bottom(1))\n # wick(m20, positive_control_l_dest)\n drop(m20)\n\n if num_samples_salmonella > 0:\n available_wells = [\n well for col in pcr_plate.columns()[num_cols_listeria:]\n for well in col]\n positive_control_s_dest = available_wells[num_samples_salmonella-2]\n pick_up_single(m20)\n m20.aspirate(5, positive_control_s.top()) # pre air gap\n m20.aspirate(vol_positive_control, positive_control_s)\n slow_withdraw(m20, positive_control_s)\n m20.dispense(m20.current_volume, positive_control_s_dest.bottom(1))\n slow_withdraw(m20, positive_control_s_dest)\n # if DO_MIX:\n # m20.mix(3, vol_positive_control*0.8,\n # positive_control_s_dest.bottom(1))\n # wick(m20, positive_control_s_dest)\n drop(m20)\n\n tempdeck.deactivate()\n", + "content": "import math\nfrom opentrons.types import Point, Mount\n\n\nmetadata = {\n 'protocolName': 'BACGene',\n 'author': 'Nick Diehl 12:\n raise Exception('Combination of listeria and salmonella samples \\\nexceeds plate capacity')\n\n # define locations of lysis buffer reagents\n lysis_buffer_listeria = lysis_rack.rows_by_name()['B'][\n 1::2]\n lysis_buffer_salmonella = lysis_rack.rows_by_name()['D'][\n 1::2]\n enzyme_listeria_1 = lysis_rack.rows_by_name()['B'][\n ::2]\n enzyme_listeria_2 = lysis_rack.rows_by_name()['C']\n enzyme_salmonella = lysis_rack.rows_by_name()['D'][\n ::2]\n positive_control_l = lysis_rack.wells_by_name()['A1']\n positive_control_s = lysis_rack.wells_by_name()['E1']\n\n # define liquids\n try:\n lysis_buffer_l_prepared_liq = ctx.define_liquid(\n name=\"listeria lysis buffer (prepared)\",\n description=\"\",\n display_color=\"#B925FF\",\n )\n lysis_buffer_l_fresh_liq = ctx.define_liquid(\n name=\"listeria lysis buffer (fresh)\",\n description=\"\",\n display_color=\"#E4ABFF\",\n )\n lysis_buffer_s_prepared_liq = ctx.define_liquid(\n name=\"salmonella lysis buffer (prepared)\",\n description=\"\",\n display_color=\"#FFD600\",\n )\n lysis_buffer_s_fresh_liq = ctx.define_liquid(\n name=\"salmonella lysis buffer (fresh)\",\n description=\"\",\n display_color=\"#FFF2AD\",\n )\n enzyme_listeria_1_liq = ctx.define_liquid(\n name=\"listeria enzyme 1\",\n description=\"\",\n display_color=\"#FF9900\",\n )\n enzyme_listeria_2_liq = ctx.define_liquid(\n name=\"listeria enzyme 2\",\n description=\"\",\n display_color=\"#9DFFD8\",\n )\n enzyme_salmonella_liq = ctx.define_liquid(\n name=\"salmonella enzyme\",\n description=\"\",\n display_color=\"#50D5FF\",\n )\n positive_control_l_liq = ctx.define_liquid(\n name=\"listeria postive control\",\n description=\"\",\n display_color=\"#FF80F5\",\n )\n positive_control_s_liq = ctx.define_liquid(\n name=\"salmonella positive control\",\n description=\"\",\n display_color=\"#7EFF42\",\n )\n samples_listeria_liq_sample = ctx.define_liquid(\n name=\"listeria samples\",\n description=\"\",\n display_color=\"#0EFFFB\",\n )\n samples_listeria_liq_lysis = ctx.define_liquid(\n name=\"listeria samples\",\n description=\"\",\n display_color=\"#0756EA\",\n )\n samples_listeria_liq_pcr = ctx.define_liquid(\n name=\"listeria samples\",\n description=\"\",\n display_color=\"#130183\",\n )\n samples_salmonella_liq_sample = ctx.define_liquid(\n name=\"salmonella samples\",\n description=\"\",\n display_color=\"#F6096D\",\n )\n samples_salmonella_liq_lysis = ctx.define_liquid(\n name=\"salmonella samples\",\n description=\"\",\n display_color=\"#FF0000\",\n )\n samples_salmonella_liq_pcr = ctx.define_liquid(\n name=\"salmonella samples\",\n description=\"\",\n display_color=\"#A92F00\",\n )\n except AttributeError:\n pass\n\n samples_single_listeria = sample_plate.wells()[:num_samples_listeria]\n num_cols_offset_samples_listeria = math.ceil(num_samples_listeria/8)\n samples_single_salmonella = sample_plate.wells()[\n num_cols_offset_samples_listeria*8:\n num_cols_offset_samples_listeria*8+num_samples_salmonella]\n lysis_single_listeria = lysis_plate.wells()[:num_samples_listeria]\n lysis_single_salmonella = lysis_plate.wells()[\n num_cols_offset_samples_listeria*8:\n num_cols_offset_samples_listeria*8+num_samples_salmonella]\n pcr_single_listeria = pcr_plate.wells()[:num_samples_listeria]\n pcr_single_salmonella = pcr_plate.wells()[\n num_cols_offset_samples_listeria*8:\n num_cols_offset_samples_listeria*8+num_samples_salmonella]\n\n # load liquids\n try:\n if num_samples_listeria > 0:\n positive_control_l.load_liquid(positive_control_l_liq, volume=10)\n if num_samples_salmonella > 0:\n positive_control_s.load_liquid(positive_control_s_liq, volume=10)\n [well.load_liquid(samples_listeria_liq_sample,\n volume=30/len(samples_single_listeria))\n for well in samples_single_listeria]\n [well.load_liquid(samples_salmonella_liq_sample,\n volume=10/len(samples_single_salmonella))\n for well in samples_single_salmonella]\n [well.load_liquid(samples_listeria_liq_lysis,\n volume=30/len(lysis_single_listeria))\n for well in lysis_single_listeria]\n [well.load_liquid(samples_salmonella_liq_lysis,\n volume=10/len(lysis_single_salmonella))\n for well in lysis_single_salmonella]\n [well.load_liquid(samples_listeria_liq_pcr,\n volume=30/len(pcr_single_listeria))\n for well in pcr_single_listeria]\n [well.load_liquid(samples_salmonella_liq_pcr,\n volume=10/len(pcr_single_salmonella))\n for well in pcr_single_salmonella]\n except AttributeError:\n pass\n\n single_tip_count_map = {m300: 0, m20: 0}\n tip_ref = m300.tip_racks[0].wells()[0]\n default_current = 1\n\n right = True\n\n def drop(pip):\n nonlocal right\n offset = 30 if right else -15\n drop_loc = ctx.loaded_labwares[12].wells()[0].top().move(\n Point(x=offset))\n pip.drop_tip(drop_loc)\n right = not right\n\n def pick_up_single(pip=m300):\n mount = Mount.LEFT if pip.mount == 'left' else Mount.RIGHT\n current_single = 1/8*default_current\n if not ctx.is_simulating():\n # attenuate pickup current\n ctx._hw_manager.hardware._attached_instruments[\n mount].update_config_item(\n 'pick_up_current', current_single)\n pip.pick_up_tip(\n [well\n for col in pip.tip_racks[-1].columns()\n for well in col[::-1]][single_tip_count_map[pip]])\n single_tip_count_map[pip] += 1\n if not ctx.is_simulating():\n # reset pickup current\n ctx._hw_manager.hardware._attached_instruments[\n mount].update_config_item('pick_up_current', default_current)\n\n def slow_withdraw(pip, well, delay_seconds=2.0, y_offset=0):\n pip.default_speed /= 10\n if delay_seconds > 0:\n ctx.delay(delay_seconds)\n pip.move_to(well.top().move(Point(y=y_offset)))\n pip.default_speed *= 10\n\n def wick(pip, well, x_magnitude=0.5, z_offset=3.0):\n radius = well.diameter/2 if well.diameter else well.width/2\n pip.default_speed /= 2\n pip.move_to(well.bottom().move(Point(x=x_magnitude*radius,\n z=z_offset)))\n pip.default_speed *= 2\n\n \"\"\" create lysis buffer with enzyme \"\"\"\n if DO_CREATE_LYSIS_BUFFER:\n\n vol_enzyme = 500.0\n num_trans = math.ceil(vol_enzyme/tip_ref.max_volume)\n vol_per_trans = round(vol_enzyme/num_trans, 1)\n\n if num_samples_listeria_remaining % 48 == 0 or \\\n num_samples_listeria_remaining % 48 == 47:\n num_partial_listeria_buffers = 0\n num_bvs_effective = 0\n else:\n num_partial_listeria_buffers = 1\n if 2*math.ceil(num_samples_listeria_remaining/2) % 48 == 0:\n num_bvs_effective = 48\n else:\n num_bvs_effective = 2*math.ceil(\n num_samples_listeria_remaining/2) % 48\n\n num_additional_listeria_buffers = math.ceil(\n ((num_samples_listeria-1) - num_bvs_effective)/48)\n\n # print(f'partial: {num_partial_listeria_buffers}')\n # print(f'additional: {num_additional_listeria_buffers}')\n\n enzyme_listeria_1_creation = enzyme_listeria_1[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]\n enzyme_listeria_2_creation = enzyme_listeria_2[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]\n lysis_buffer_listeria_creation = lysis_buffer_listeria[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers+num_additional_listeria_buffers]\n # print(lysis_buffer_listeria_creation)\n\n # load partial liq\n if num_samples_listeria > 0:\n try:\n [\n well.load_liquid(\n lysis_buffer_l_prepared_liq,\n volume=11000/num_partial_listeria_buffers)\n for well in lysis_buffer_listeria[\n :num_partial_listeria_buffers]]\n\n # load full liq\n [\n well.load_liquid(\n lysis_buffer_l_fresh_liq,\n volume=11000/num_additional_listeria_buffers)\n for well in lysis_buffer_listeria[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers +\n num_additional_listeria_buffers]]\n [\n well.load_liquid(\n enzyme_listeria_1_liq,\n volume=500/num_additional_listeria_buffers)\n for well in enzyme_listeria_1[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers +\n num_additional_listeria_buffers]]\n [\n well.load_liquid(\n enzyme_listeria_2_liq,\n volume=500/num_additional_listeria_buffers)\n for well in enzyme_listeria_2[\n num_partial_listeria_buffers:\n num_partial_listeria_buffers +\n num_additional_listeria_buffers]]\n except AttributeError:\n pass\n\n # listeria\n for enzyme1, enzyme2, lysis_buff in zip(\n enzyme_listeria_1_creation,\n enzyme_listeria_2_creation,\n lysis_buffer_listeria_creation):\n # enzyme 1\n pick_up_single(m300)\n for _ in range(num_trans):\n m300.aspirate(\n vol_per_trans, enzyme1.bottom().move(\n Point(x=OFFSET_X_TUBERACK, z=1)))\n slow_withdraw(m300, enzyme1)\n m300.move_to(\n lysis_buff.top().move(\n Point(x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA)))\n m300.dispense(\n vol_per_trans,\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=3)))\n m300.blow_out()\n slow_withdraw(\n m300, lysis_buff, y_offset=OFFSET_Y_LYSIS_BUFFER_LISTERIA)\n drop(m300)\n\n # enzyme 2\n pick_up_single(m300)\n for i in range(num_trans):\n m300.aspirate(\n vol_per_trans, enzyme2.bottom().move(\n Point(x=OFFSET_X_TUBERACK, z=1)))\n slow_withdraw(m300, enzyme2)\n m300.move_to(\n lysis_buff.top().move(Point(\n x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA)))\n m300.dispense(\n vol_per_trans,\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=3)))\n if i == num_trans - 1:\n if DO_MIX:\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n m300.mix(\n 10, 200,\n lysis_buff.bottom().move(Point(\n x=OFFSET_X_TUBERACK,\n z=3, y=OFFSET_Y_LYSIS_BUFFER_LISTERIA)))\n m300.flow_rate.aspirate /= 2\n m300.flow_rate.dispense /= 2\n m300.blow_out(\n lysis_buff.bottom().move(Point(\n x=OFFSET_X_TUBERACK,\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA, z=3)))\n slow_withdraw(\n m300, lysis_buff, y_offset=OFFSET_Y_LYSIS_BUFFER_LISTERIA)\n drop(m300)\n\n # salmonella\n if num_samples_salmonella_remaining % 48 == 0 or \\\n num_samples_salmonella_remaining == 47:\n num_partial_salmonella_buffers = 0\n num_bvs_effective = 0\n else:\n num_partial_salmonella_buffers = 1\n if 2*math.ceil(num_samples_salmonella_remaining/2) % 48 == 0:\n num_bvs_effective = 48\n else:\n num_bvs_effective = 2*math.ceil(\n num_samples_salmonella_remaining/2) % 48\n\n num_additional_salmonella_buffers = math.ceil(\n ((num_samples_salmonella-1) - num_bvs_effective)/48)\n\n enzyme_salmonella_creation = enzyme_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers+num_additional_salmonella_buffers]\n lysis_buffer_salmonella_creation = lysis_buffer_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers+num_additional_salmonella_buffers]\n\n # load partial liq\n if num_samples_listeria > 0:\n try:\n [\n well.load_liquid(\n lysis_buffer_s_prepared_liq,\n volume=11000/num_partial_salmonella_buffers)\n for well in lysis_buffer_salmonella[\n :num_partial_salmonella_buffers]]\n\n # load full liq\n [\n well.load_liquid(\n lysis_buffer_s_fresh_liq,\n volume=11000/num_additional_salmonella_buffers)\n for well in lysis_buffer_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers +\n num_additional_salmonella_buffers]]\n [\n well.load_liquid(\n enzyme_salmonella_liq,\n volume=500/num_additional_salmonella_buffers)\n for well in enzyme_salmonella[\n num_partial_salmonella_buffers:\n num_partial_salmonella_buffers +\n num_additional_salmonella_buffers]]\n except AttributeError:\n pass\n\n for enzyme, lysis_buff in zip(enzyme_salmonella_creation,\n lysis_buffer_salmonella_creation):\n # enzyme\n pick_up_single(m300)\n for i in range(num_trans):\n m300.aspirate(vol_per_trans, enzyme.bottom().move(\n Point(x=OFFSET_X_TUBERACK, z=1)))\n slow_withdraw(m300, enzyme)\n m300.move_to(\n lysis_buff.top().move(\n Point(x=OFFSET_X_TUBERACK,\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)))\n m300.dispense(\n vol_per_trans,\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=3)))\n if i == num_trans - 1:\n if DO_MIX:\n m300.flow_rate.aspirate *= 2\n m300.flow_rate.dispense *= 2\n m300.mix(\n 10, 200,\n lysis_buff.bottom().move(Point(\n x=OFFSET_X_TUBERACK,\n z=3, y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)))\n m300.flow_rate.aspirate /= 2\n m300.flow_rate.dispense /= 2\n m300.blow_out(\n lysis_buff.bottom().move(\n Point(x=OFFSET_X_TUBERACK,\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=3)))\n slow_withdraw(\n m300, lysis_buff,\n y_offset=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)\n drop(m300)\n\n \"\"\" transfer lysis buffer to lysis plate \"\"\"\n vol_overage = 20\n\n if num_samples_listeria > 0:\n if DO_DISTRIBUTE_LYSIS_BUFFER:\n lysis_buffer_listeria_dests = lysis_plate.wells()[\n :num_samples_listeria-2] + [\n lysis_plate.wells()[num_samples_listeria-1]]\n vol_lysis_buffer_listeria = 70.0\n num_dests_per_asp = int(\n (tip_ref.max_volume-vol_overage)//vol_lysis_buffer_listeria)\n num_asp = math.ceil(\n len(lysis_buffer_listeria_dests)/num_dests_per_asp)\n lysis_buffer_listeria_dest_sets = [\n lysis_buffer_listeria_dests[i*num_dests_per_asp:\n (i+1)*num_dests_per_asp]\n if i < num_asp - 1\n else lysis_buffer_listeria_dests[i*num_dests_per_asp:]\n for i in range(num_asp)]\n pick_up_single(m300)\n m300.aspirate(\n vol_overage,\n lysis_buffer_listeria[0].bottom().move(Point(\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=OFFSET_Z_LYSIS_BUFFER_LISTERIA)))\n num_asp_listeria_remaining = math.ceil(\n (num_samples_listeria_remaining % 48) / 2)\n bump = 24 - num_asp_listeria_remaining \\\n if 24 - num_asp_listeria_remaining != 24 else 0\n for i, d_set in enumerate(lysis_buffer_listeria_dest_sets):\n set_ind = i + bump\n lysis_buff = lysis_buffer_listeria[set_ind//24]\n # m300.blow_out(lysis_buff.top(-1))\n m300.aspirate(\n len(d_set)*vol_lysis_buffer_listeria,\n lysis_buff.bottom().move(Point(\n y=OFFSET_Y_LYSIS_BUFFER_LISTERIA,\n z=OFFSET_Z_LYSIS_BUFFER_LISTERIA)))\n slow_withdraw(\n m300, lysis_buff, y_offset=OFFSET_Y_LYSIS_BUFFER_LISTERIA)\n for d in d_set:\n m300.dispense(vol_lysis_buffer_listeria, d.bottom(2))\n slow_withdraw(m300, d)\n drop(m300)\n\n if num_samples_salmonella > 0:\n if DO_DISTRIBUTE_LYSIS_BUFFER:\n available_wells = [\n well for col in lysis_plate.columns()[num_cols_listeria:]\n for well in col]\n lysis_buffer_salmonella_dests = available_wells[\n :num_samples_salmonella-2] + [\n available_wells[num_samples_salmonella-1]]\n vol_lysis_buffer_salmonella = 90.0 if not salmonella_meat else 50.0\n num_dests_per_asp = 2 # hard-set for now\n num_asp = math.ceil(\n len(lysis_buffer_salmonella_dests)/num_dests_per_asp)\n lysis_buffer_salmonella_dest_sets = [\n lysis_buffer_salmonella_dests[i*num_dests_per_asp:\n (i+1)*num_dests_per_asp]\n if i < num_asp - 1\n else lysis_buffer_salmonella_dests[i*num_dests_per_asp:]\n for i in range(num_asp)]\n pick_up_single(m300)\n m300.aspirate(\n vol_overage,\n lysis_buffer_salmonella[0].bottom().move(\n Point(y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=OFFSET_Z_LYSIS_BUFFER_SALMONELLA)))\n num_asp_salmonella_remaining = math.ceil(\n (num_samples_salmonella_remaining % 48) / 2)\n bump_check = int(48/num_dests_per_asp)\n bump = bump_check - num_asp_salmonella_remaining \\\n if bump_check - num_asp_salmonella_remaining != bump_check \\\n else 0\n for i, d_set in enumerate(lysis_buffer_salmonella_dest_sets):\n set_ind = i + bump\n lysis_buff = lysis_buffer_salmonella[set_ind//bump_check]\n # m300.blow_out(lysis_buff.top(-1))\n # print('salmonella', i, set_ind, lysis_buff, len(d_set))\n # m300.blow_out(lysis_buff.top(-1))\n m300.aspirate(\n len(d_set)*vol_lysis_buffer_salmonella,\n lysis_buff.bottom().move(Point(\n y=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA,\n z=OFFSET_Z_LYSIS_BUFFER_SALMONELLA)))\n slow_withdraw(m300, lysis_buff,\n y_offset=-OFFSET_Y_LYSIS_BUFFER_SALMONELLA)\n for d in d_set:\n m300.dispense(vol_lysis_buffer_salmonella, d.bottom(2))\n slow_withdraw(m300, d)\n drop(m300)\n\n if DO_TRANSFER_SAMPLE_TO_LYSIS:\n \"\"\" transfer listeria \"\"\"\n vol_listeria = 30.0\n num_sample_cols_listeria = math.ceil((num_samples_listeria-2)/8)\n for s, d in zip(sample_plate.rows()[0][:num_sample_cols_listeria],\n lysis_plate.rows()[0][:num_sample_cols_listeria]):\n if sample_rack_type == 'bioplastics':\n asp_loc = s.bottom(2)\n else:\n asp_loc = s.top(-17.36)\n m300.pick_up_tip()\n m300.aspirate(vol_listeria, asp_loc)\n slow_withdraw(m300, s)\n m300.dispense(vol_listeria, d.bottom(2))\n if DO_MIX:\n m300.mix(3, 50, d.bottom(2))\n m300.blow_out(d.bottom(2))\n slow_withdraw(m300, d)\n drop(m300)\n\n \"\"\" transfer salmonella \"\"\"\n [pip, vol_salmonella] = [m20, 10.0] \\\n if not salmonella_meat else [m300, 50.0]\n num_cols_samples_salmonella = math.ceil((num_samples_salmonella-2)/8)\n for s, d in zip(\n sample_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_samples_salmonella],\n lysis_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_samples_salmonella]):\n pip.pick_up_tip()\n if sample_rack_type == 'bioplastics':\n asp_loc = s.bottom(2)\n else:\n asp_loc = s.top(-17.36)\n pip.aspirate(vol_salmonella, asp_loc)\n slow_withdraw(pip, s)\n pip.dispense(vol_salmonella, d.bottom(2))\n if DO_MIX:\n pip.mix(3, 18, d.bottom(2))\n pip.blow_out(d.bottom(2))\n slow_withdraw(pip, d)\n drop(pip)\n\n if DO_SET_TEMP:\n ctx.delay(minutes=20, msg='Incubating for 20 minutes @ 37C.')\n tempdeck.set_temperature(95)\n ctx.delay(minutes=10, msg='Incubating for 10 minutes @ 95C.')\n tempdeck.set_temperature(37)\n\n vol_sample = 5.0\n\n if DO_TRANSFER_SAMPLE_TO_PCR:\n \"\"\" transfer samples to PCR plate \"\"\"\n\n # listeria\n if num_samples_listeria > 0:\n for s, d in zip(lysis_plate.rows()[0][:num_cols_listeria],\n pcr_plate.rows()[0][:num_cols_listeria]):\n m20.pick_up_tip()\n m20.aspirate(5, s.top()) # pre air gap\n m20.aspirate(vol_sample, s)\n slow_withdraw(m20, s)\n m20.dispense(vol_sample, d.bottom(1))\n # if DO_MIX:\n # m20.mix(3, vol_sample*0.8, d.bottom(1))\n m20.dispense(m20.current_volume, d.bottom(1))\n slow_withdraw(m20, d)\n # wick(m20, d)\n drop(m20)\n\n # salmonella\n if num_samples_salmonella > 0:\n for s, d in zip(\n lysis_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_salmonella],\n pcr_plate.rows()[0][\n num_cols_listeria:\n num_cols_listeria+num_cols_salmonella]):\n m20.pick_up_tip()\n m20.aspirate(5, s.top()) # pre air gap\n m20.aspirate(vol_sample, s)\n slow_withdraw(m20, s)\n m20.dispense(vol_sample, d.bottom(1))\n # if DO_MIX:\n # m20.mix(3, vol_sample*0.8, d.bottom(1))\n m20.dispense(m20.current_volume, d.bottom(1))\n slow_withdraw(m20, d)\n m20.air_gap(5)\n # wick(m20, d)\n drop(m20)\n\n if DO_TRANSFER_POSITIVE_CONTROL:\n \"\"\" transfer positive controls \"\"\"\n vol_positive_control = vol_sample\n if num_samples_listeria > 0:\n positive_control_l_dest = pcr_plate.wells()[num_samples_listeria-2]\n pick_up_single(m20)\n m20.aspirate(5, positive_control_l_dest.top()) # pre air gap\n m20.aspirate(vol_positive_control, positive_control_l)\n slow_withdraw(m20, positive_control_l)\n m20.dispense(m20.current_volume, positive_control_l_dest.bottom(1))\n slow_withdraw(m20, positive_control_l_dest)\n # if DO_MIX:\n # m20.mix(3, vol_positive_control*0.8,\n # positive_control_l_dest.bottom(1))\n # wick(m20, positive_control_l_dest)\n drop(m20)\n\n if num_samples_salmonella > 0:\n available_wells = [\n well for col in pcr_plate.columns()[num_cols_listeria:]\n for well in col]\n positive_control_s_dest = available_wells[num_samples_salmonella-2]\n pick_up_single(m20)\n m20.aspirate(5, positive_control_s.top()) # pre air gap\n m20.aspirate(vol_positive_control, positive_control_s)\n slow_withdraw(m20, positive_control_s)\n m20.dispense(m20.current_volume, positive_control_s_dest.bottom(1))\n slow_withdraw(m20, positive_control_s_dest)\n # if DO_MIX:\n # m20.mix(3, vol_positive_control*0.8,\n # positive_control_s_dest.bottom(1))\n # wick(m20, positive_control_s_dest)\n drop(m20)\n\n tempdeck.deactivate()\n", "custom_labware_defs": [ { "brand": { diff --git a/protocols/gsdx/bacgene.ot2.apiv2.py b/protocols/gsdx/bacgene.ot2.apiv2.py index 343fe5987..aa27099a6 100644 --- a/protocols/gsdx/bacgene.ot2.apiv2.py +++ b/protocols/gsdx/bacgene.ot2.apiv2.py @@ -299,33 +299,42 @@ def wick(pip, well, x_magnitude=0.5, z_offset=3.0): # print(lysis_buffer_listeria_creation) # load partial liq - try: - [well.load_liquid( - lysis_buffer_l_prepared_liq, - volume=11000/num_partial_listeria_buffers) - for well in lysis_buffer_listeria[:num_partial_listeria_buffers]] - - # load full liq - [well.load_liquid( - lysis_buffer_l_fresh_liq, - volume=11000/num_additional_listeria_buffers) - for well in lysis_buffer_listeria[ - num_partial_listeria_buffers: - num_partial_listeria_buffers+num_additional_listeria_buffers]] - [well.load_liquid( - enzyme_listeria_1_liq, - volume=500/num_additional_listeria_buffers) - for well in enzyme_listeria_1[ - num_partial_listeria_buffers: - num_partial_listeria_buffers+num_additional_listeria_buffers]] - [well.load_liquid( - enzyme_listeria_2_liq, - volume=500/num_additional_listeria_buffers) - for well in enzyme_listeria_2[ - num_partial_listeria_buffers: - num_partial_listeria_buffers+num_additional_listeria_buffers]] - except AttributeError: - pass + if num_samples_listeria > 0: + try: + [ + well.load_liquid( + lysis_buffer_l_prepared_liq, + volume=11000/num_partial_listeria_buffers) + for well in lysis_buffer_listeria[ + :num_partial_listeria_buffers]] + + # load full liq + [ + well.load_liquid( + lysis_buffer_l_fresh_liq, + volume=11000/num_additional_listeria_buffers) + for well in lysis_buffer_listeria[ + num_partial_listeria_buffers: + num_partial_listeria_buffers + + num_additional_listeria_buffers]] + [ + well.load_liquid( + enzyme_listeria_1_liq, + volume=500/num_additional_listeria_buffers) + for well in enzyme_listeria_1[ + num_partial_listeria_buffers: + num_partial_listeria_buffers + + num_additional_listeria_buffers]] + [ + well.load_liquid( + enzyme_listeria_2_liq, + volume=500/num_additional_listeria_buffers) + for well in enzyme_listeria_2[ + num_partial_listeria_buffers: + num_partial_listeria_buffers + + num_additional_listeria_buffers]] + except AttributeError: + pass # listeria for enzyme1, enzyme2, lysis_buff in zip( @@ -414,30 +423,34 @@ def wick(pip, well, x_magnitude=0.5, z_offset=3.0): num_partial_salmonella_buffers+num_additional_salmonella_buffers] # load partial liq - try: - [well.load_liquid( - lysis_buffer_s_prepared_liq, - volume=11000/num_partial_salmonella_buffers) - for well in lysis_buffer_salmonella[ - :num_partial_salmonella_buffers]] - - # load full liq - [well.load_liquid( - lysis_buffer_s_fresh_liq, - volume=11000/num_additional_salmonella_buffers) - for well in lysis_buffer_salmonella[ - num_partial_salmonella_buffers: - num_partial_salmonella_buffers + - num_additional_salmonella_buffers]] - [well.load_liquid( - enzyme_salmonella_liq, - volume=500/num_additional_salmonella_buffers) - for well in enzyme_salmonella[ - num_partial_salmonella_buffers: - num_partial_salmonella_buffers + - num_additional_salmonella_buffers]] - except AttributeError: - pass + if num_samples_listeria > 0: + try: + [ + well.load_liquid( + lysis_buffer_s_prepared_liq, + volume=11000/num_partial_salmonella_buffers) + for well in lysis_buffer_salmonella[ + :num_partial_salmonella_buffers]] + + # load full liq + [ + well.load_liquid( + lysis_buffer_s_fresh_liq, + volume=11000/num_additional_salmonella_buffers) + for well in lysis_buffer_salmonella[ + num_partial_salmonella_buffers: + num_partial_salmonella_buffers + + num_additional_salmonella_buffers]] + [ + well.load_liquid( + enzyme_salmonella_liq, + volume=500/num_additional_salmonella_buffers) + for well in enzyme_salmonella[ + num_partial_salmonella_buffers: + num_partial_salmonella_buffers + + num_additional_salmonella_buffers]] + except AttributeError: + pass for enzyme, lysis_buff in zip(enzyme_salmonella_creation, lysis_buffer_salmonella_creation): From 02f53fe6e990f073a76189daea7a4ddb39e297ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Wed, 6 Sep 2023 14:18:09 -0400 Subject: [PATCH 4/6] fix --- protocols/0c24ca/0c24ca.ot2.apiv2.py | 2 +- protocols/0c24ca/fields.json | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/protocols/0c24ca/0c24ca.ot2.apiv2.py b/protocols/0c24ca/0c24ca.ot2.apiv2.py index bc28097d2..09df2dc27 100644 --- a/protocols/0c24ca/0c24ca.ot2.apiv2.py +++ b/protocols/0c24ca/0c24ca.ot2.apiv2.py @@ -87,7 +87,7 @@ def adjust_height(vol): dest_well = dest_slot.wells_by_name()[dest_well_name] pick_up(pip) - pip.aspirate(remove_tube_vol, source_well) + pip.aspirate(remove_tube_vol, source_well.bottom(z=2)) pip.dispense(remove_tube_vol, dest_well) pip.drop_tip() diff --git a/protocols/0c24ca/fields.json b/protocols/0c24ca/fields.json index eee9c3780..6032252c8 100644 --- a/protocols/0c24ca/fields.json +++ b/protocols/0c24ca/fields.json @@ -27,7 +27,7 @@ ] }, { - "type": "int", + "type": "float", "label": "Sample tube removal volume", "name": "remove_tube_vol", "default": 20 @@ -51,13 +51,13 @@ ] }, { - "type": "int", + "type": "float", "label": "Transfection mix volume", "name": "trans_mix_vol", "default": 40 }, { - "type": "int", + "type": "float", "label": "Initial volume of transfection mix in 50mL tube (mL)", "name": "init_vol_50", "default": 40 From 8b8c1ddca5c624607368c673696c486d4b6bc4ef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Wed, 6 Sep 2023 14:18:27 -0400 Subject: [PATCH 5/6] fix --- protoBuilds/0045f1/README.json | 2 +- protoBuilds/00a214-protocol-1/README.json | 2 +- protoBuilds/00a214-protocol-2/README.json | 2 +- protoBuilds/00a214-protocol-3/README.json | 2 +- protoBuilds/00a214-protocol-4/README.json | 2 +- protoBuilds/00a214-protocol-5/README.json | 2 +- protoBuilds/00a6e5/README.json | 2 +- protoBuilds/00bbd7/README.json | 2 +- protoBuilds/010526/README.json | 2 +- protoBuilds/017860/README.json | 2 +- protoBuilds/019a7d_part_2/README.json | 2 +- protoBuilds/022548-2/README.json | 2 +- protoBuilds/022548/README.json | 2 +- protoBuilds/02pnzp/README.json | 2 +- protoBuilds/04eeb1-part-2/README.json | 2 +- protoBuilds/04eeb1-part-3/README.json | 2 +- protoBuilds/04eeb1-part-4/README.json | 2 +- protoBuilds/04eeb1-part-5/README.json | 2 +- protoBuilds/04eeb1-part-6/README.json | 2 +- protoBuilds/04eeb1-part-7/README.json | 2 +- protoBuilds/04eeb1/README.json | 2 +- protoBuilds/04f310/README.json | 2 +- protoBuilds/04f4e7/README.json | 2 +- protoBuilds/055b94/README.json | 2 +- protoBuilds/059126/README.json | 2 +- protoBuilds/05f673/README.json | 2 +- protoBuilds/060c4f/README.json | 2 +- protoBuilds/063611-part-2/README.json | 2 +- protoBuilds/063611/README.json | 2 +- protoBuilds/06da40/README.json | 2 +- protoBuilds/08878b/README.json | 2 +- protoBuilds/089108/README.json | 2 +- protoBuilds/08e3eb/README.json | 2 +- protoBuilds/0944e4/README.json | 2 +- protoBuilds/0a33e8/README.json | 2 +- protoBuilds/0add76/README.json | 2 +- protoBuilds/0aee8a/README.json | 2 +- protoBuilds/0b97ae-protocol-2A/README.json | 2 +- protoBuilds/0b97ae-protocol-2B/README.json | 2 +- protoBuilds/0b97ae-protocol-3B/README.json | 2 +- protoBuilds/0b97ae/README.json | 2 +- protoBuilds/0b98cc/README.json | 2 +- protoBuilds/0bf4f4-pt2/README.json | 2 +- protoBuilds/0bf4f4-pt3/README.json | 2 +- protoBuilds/0bf4f4/README.json | 2 +- protoBuilds/0c24ca/0c24ca.ot2.apiv2.py.json | 8 ++++---- protoBuilds/0cded6-amplify/README.json | 2 +- protoBuilds/0cded6-amplify2/README.json | 2 +- protoBuilds/0cded6-cleanup/README.json | 2 +- protoBuilds/0cded6-synthesize/README.json | 2 +- protoBuilds/0cded6-tagment/README.json | 2 +- protoBuilds/0cded6/README.json | 2 +- protoBuilds/0d2950/README.json | 2 +- protoBuilds/0e7175-pt2/README.json | 2 +- protoBuilds/0e7175/README.json | 2 +- protoBuilds/0e8e3/README.json | 2 +- protoBuilds/0eaeb5/README.json | 2 +- protoBuilds/0f4405/README.json | 2 +- protoBuilds/0f5985/README.json | 2 +- protoBuilds/0fa015/README.json | 2 +- protoBuilds/0ff0c3/README.json | 2 +- protoBuilds/10bf60-station-B/README.json | 2 +- protoBuilds/111210-part-10/README.json | 2 +- protoBuilds/111210-part-2/README.json | 2 +- protoBuilds/111210-part-3/README.json | 2 +- protoBuilds/111210-part-4/README.json | 2 +- protoBuilds/111210-part-5/README.json | 2 +- protoBuilds/111210-part-6/README.json | 2 +- protoBuilds/111210-part-7/README.json | 2 +- 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protoBuilds/rem-pcr-plate/README.json | 2 +- protoBuilds/sci-amplex-red/README.json | 2 +- protoBuilds/sci-dynabeads-tube-1/README.json | 2 +- protoBuilds/sci-dynabeads-tube-2/README.json | 2 +- protoBuilds/sci-idt-normalase/README.json | 2 +- protoBuilds/sci-idt-xgen-ez/README.json | 2 +- protoBuilds/sci-idt-xgen-mc/README.json | 4 ++-- protoBuilds/sci-illumina-dna-prep/README.json | 2 +- protoBuilds/sci-macherey-nagel-nucleomag/README.json | 2 +- protoBuilds/sci-mag-bind-blood-tissue-kit/README.json | 2 +- protoBuilds/sci-neb-next-ultra/README.json | 2 +- protoBuilds/sci-omegabiotek-extraction-fa/README.json | 2 +- protoBuilds/sci-omegabiotek-extraction/README.json | 2 +- protoBuilds/sci-omegabiotek-magbind-temp/README.json | 2 +- .../sci-omegabiotek-magbind-total-rna-96/README.json | 2 +- protoBuilds/sci-omegabiotek-magbind/README.json | 2 +- protoBuilds/sci-phytip-plate-prep/README.json | 2 +- protoBuilds/sci-phytip-protein-A/README.json | 2 +- protoBuilds/sci-phytip-protein-puri/README.json | 2 +- .../sci-promega-magazorb-dna-mini-prep-kit/README.json | 2 +- protoBuilds/sci-roche-hyperprep/README.json | 2 +- protoBuilds/sci-thermofisher-magmax/README.json | 4 ++-- protoBuilds/sci-zymo-directzol-magbead/README.json | 2 +- protoBuilds/swift-2s-turbo-pt1/README.json | 2 +- protoBuilds/swift-2s-turbo-pt2/README.json | 2 +- protoBuilds/swift-2s-turbo-pt3/README.json | 2 +- protoBuilds/swift-fully-automated-custom/README.json | 2 +- protoBuilds/swift-fully-automated/README.json | 2 +- protoBuilds/testdrive/README.json | 2 +- protoBuilds/thermocycler/README.json | 2 +- protoBuilds/zymo-quick-custom/README.json | 2 +- protoBuilds/zymo-quick/README.json | 2 +- protoBuilds/zymo-ribofree-cleanup/README.json | 2 +- .../README.json | 2 +- protoBuilds/zymo-ribofree-library-index-pcr/README.json | 2 +- protoBuilds/zymo-ribofree-p5-adapter-ligation/README.json | 2 +- protoBuilds/zymo-ribofree-p7-adapter-ligation/README.json | 2 +- protoBuilds/zymo-rna-extraction/README.json | 2 +- 456 files changed, 482 insertions(+), 482 deletions(-) diff --git a/protoBuilds/0045f1/README.json b/protoBuilds/0045f1/README.json index 0a7525f4e..bf7d470a6 100644 --- a/protoBuilds/0045f1/README.json +++ b/protoBuilds/0045f1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol spots up to 6 slides with antibody. Each slide has 8 wells, to which the protocol will spot with 8 dots for wells 2-7. The user has the ability to manipulate the spacing between the dots, as well as the volume of the dispenses. The user can also specify the number of slides spotted. Please see below for the order in which slides are spotted.\nExplanation of complex parameters below:\n* Number of tubes: Specify the number of tubes this protocol will run.\n* Number of Slides: Specify the number of slides for this run (1-6).\n* Spot Spacing: Specify the spacing between dots on the slide wells.\n* Spot Volume: Specify the volume of each dot.\n* Aspiration Flow Rate: Specify the aspiration rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* Dispense Flow Rate: Specify the dispense rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* P20 Single-Channel Mount: Specify which mount (left or right) to host the P20 single-channel pipette.\n", + "description": "This protocol spots up to 6 slides with antibody. Each slide has 8 wells, to which the protocol will spot with 8 dots for wells 2-7. The user has the ability to manipulate the spacing between the dots, as well as the volume of the dispenses. The user can also specify the number of slides spotted. Please see below for the order in which slides are spotted.\nExplanation of complex parameters below:\n Number of tubes: Specify the number of tubes this protocol will run.\n Number of Slides: Specify the number of slides for this run (1-6).\n Spot Spacing: Specify the spacing between dots on the slide wells.\n Spot Volume: Specify the volume of each dot.\n Aspiration Flow Rate: Specify the aspiration rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n Dispense Flow Rate: Specify the dispense rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* P20 Single-Channel Mount: Specify which mount (left or right) to host the P20 single-channel pipette.\n", "internal": "0045f1", "labware": "\nOpentrons 10ul filter tips\nOpentrons 4-in-1 tube rack with Eppendorf 1.5mL safelock snapcap\nCustom slide plate\n", "markdown": { diff --git a/protoBuilds/00a214-protocol-1/README.json b/protoBuilds/00a214-protocol-1/README.json index f33b9582a..398157777 100644 --- a/protoBuilds/00a214-protocol-1/README.json +++ b/protoBuilds/00a214-protocol-1/README.json @@ -5,7 +5,7 @@ "Seeding Plate" ] }, - "description": "This protocol automates seeding plates with mammalian cells and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 8 plates, the protocol will iterate through each plate and remove 50\u00b5L before adding 140\u00b5L from the reservoir. Each plate should have a designated well in the 12-well trough (i.e., slot 1 --> plate 1, slot 2 --> plate 2, etc.)\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Eppendorf Plate (Plate 3)\n\nSlot 5: Eppendorf Plate (Plate 4)\n\nSlot 6: Eppendorf Plate (Plate 5)\n\nSlot 7: Eppendorf Plate (Plate 6)\n\nSlot 8: Eppendorf Plate (Plate 7)\n\nSlot 9: Eppendorf Plate (Plate 8)\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-8) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", + "description": "This protocol automates seeding plates with mammalian cells and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 8 plates, the protocol will iterate through each plate and remove 50\u00b5L before adding 140\u00b5L from the reservoir. Each plate should have a designated well in the 12-well trough (i.e., slot 1 --> plate 1, slot 2 --> plate 2, etc.)\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Eppendorf Plate (Plate 3)\n\nSlot 5: Eppendorf Plate (Plate 4)\n\nSlot 6: Eppendorf Plate (Plate 5)\n\nSlot 7: Eppendorf Plate (Plate 6)\n\nSlot 8: Eppendorf Plate (Plate 7)\n\nSlot 9: Eppendorf Plate (Plate 8)\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-8) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", "internal": "00a214-protocol-1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/00a214-protocol-2/README.json b/protoBuilds/00a214-protocol-2/README.json index 768c663b6..5fe01c363 100644 --- a/protoBuilds/00a214-protocol-2/README.json +++ b/protoBuilds/00a214-protocol-2/README.json @@ -5,7 +5,7 @@ "Staining" ] }, - "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-4) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", + "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-4) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", "internal": "00a214-protocol-2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/00a214-protocol-3/README.json b/protoBuilds/00a214-protocol-3/README.json index d43f9c3b7..f1f468b01 100644 --- a/protoBuilds/00a214-protocol-3/README.json +++ b/protoBuilds/00a214-protocol-3/README.json @@ -5,7 +5,7 @@ "Staining" ] }, - "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-4) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", + "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-4) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", "internal": "00a214-protocol-3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/00a214-protocol-4/README.json b/protoBuilds/00a214-protocol-4/README.json index d0ac69e8f..1aa5cd520 100644 --- a/protoBuilds/00a214-protocol-4/README.json +++ b/protoBuilds/00a214-protocol-4/README.json @@ -5,7 +5,7 @@ "Staining" ] }, - "description": "This protocol automates Media Exchange and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of differentiation media\nIf necessary (can select 'yes' or 'no' under Second Exchange)\nRemove 140\u00b5L of differentiation media\nAdd 140\u00b5L of differentiation media\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Eppendorf Plate (Plate 3)\n\nSlot 5: Eppendorf Plate (Plate 4)\n\nSlot 5: Eppendorf Plate (Plate 5)\n\nSlot 6: Eppendorf Plate (Plate 6)\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-6: Differentiation Media (for 1st exchange)\nColumns 7-22: Differentiation Media (for 2nd exchange)\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 6 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1 and 2 would be filled with differentiation media. If also doing the second exchange, then columns 7 and 8 would also need to be filled.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-4) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n* Second Exchange: Select whether or not to perform a second exchange of differentiation media.\n\n", + "description": "This protocol automates Media Exchange and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of differentiation media\nIf necessary (can select 'yes' or 'no' under Second Exchange)\nRemove 140\u00b5L of differentiation media\nAdd 140\u00b5L of differentiation media\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Eppendorf Plate (Plate 3)\n\nSlot 5: Eppendorf Plate (Plate 4)\n\nSlot 5: Eppendorf Plate (Plate 5)\n\nSlot 6: Eppendorf Plate (Plate 6)\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-6: Differentiation Media (for 1st exchange)\nColumns 7-22: Differentiation Media (for 2nd exchange)\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 6 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1 and 2 would be filled with differentiation media. If also doing the second exchange, then columns 7 and 8 would also need to be filled.\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-4) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n* Second Exchange: Select whether or not to perform a second exchange of differentiation media.\n\n", "internal": "00a214-protocol-4", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/00a214-protocol-5/README.json b/protoBuilds/00a214-protocol-5/README.json index bdbe8f037..ee5d8a080 100644 --- a/protoBuilds/00a214-protocol-5/README.json +++ b/protoBuilds/00a214-protocol-5/README.json @@ -5,7 +5,7 @@ "Staining" ] }, - "description": "This protocol automates primary staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBST\nPause\nRemove 140\u00b5L of PBST\nAdd 140\u00b5L of Blocking Buffer\nPause\nRemove 140\u00b5L of Blocking Buffer\nAdd 140\u00b5L of Primary Antibody\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBST\nColumns 5-8: Blocking Buffer\nColumns 9-12: Primary Antibody\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-4) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", + "description": "This protocol automates primary staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBST\nPause\nRemove 140\u00b5L of PBST\nAdd 140\u00b5L of Blocking Buffer\nPause\nRemove 140\u00b5L of Blocking Buffer\nAdd 140\u00b5L of Primary Antibody\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBST\nColumns 5-8: Blocking Buffer\nColumns 9-12: Primary Antibody\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-4) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n", "internal": "00a214-protocol-5", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/00a6e5/README.json b/protoBuilds/00a6e5/README.json index 1d19d4402..c2713274a 100644 --- a/protoBuilds/00a6e5/README.json +++ b/protoBuilds/00a6e5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol preps a 96 well plate for an LCMS extraction. The 96 well plate is loaded with negative urine samples. Reagents include enzyme, buffer, water, and spike INSTD. All transfers in the 96 well plate are by column. No mix steps are included and a 30 minute pause is included after water is added to the plate.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples (1-96) for this protocol.\n* P300 Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n* Aspiration height: Specify the aspiration height for this run. A value of 1mm is the default from the bottom of the well. \n* P1000 Mount: Specify which mount (left or right) to host the P1000 single-channel pipette.\n", + "description": "This protocol preps a 96 well plate for an LCMS extraction. The 96 well plate is loaded with negative urine samples. Reagents include enzyme, buffer, water, and spike INSTD. All transfers in the 96 well plate are by column. No mix steps are included and a 30 minute pause is included after water is added to the plate.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples (1-96) for this protocol.\n P300 Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n Aspiration height: Specify the aspiration height for this run. A value of 1mm is the default from the bottom of the well. \n P1000 Mount: Specify which mount (left or right) to host the P1000 single-channel pipette.\n", "internal": "00a6e5", "labware": "\nOpentrons 4-in-1 tube rack\nOpentrons 1000ul tips\nOpentrons 300ul Tips\nNEST 12-Well Reservoir, 15mL\nAgilent 1 Well Reservoir, 290mL\nCustom 96 well plate\n", "markdown": { diff --git a/protoBuilds/00bbd7/README.json b/protoBuilds/00bbd7/README.json index e125d6d04..828184a5e 100644 --- a/protoBuilds/00bbd7/README.json +++ b/protoBuilds/00bbd7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Samples should be placed in tube racks by row (A1, A2, etc.) and by slot order 4, 5, 6, 7, 8, 9, 10.\n\n", - "description": "This protocol preps a 96 well plate with Covid-19 saliva samples in up to 7 tube racks. Delays are inserted after aspiration to ensure the full volume of sample is achieved, as well as giving the user the ability to manipulate aspiration and dispense speeds.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples for this run.\n* Delay After Aspiration (seconds): Specify the number of seconds after aspirating Covid sample to allow time for the full volume to be achieved.\n* Aspiration/Dispense Speed: Specify the speed at which to aspirate/dispense Covid sample. A value of 1 is the default speed, a value of 0.5 is half of the default speed, etc.\n* P1000 Single GEN2 Mount: Specify whether the P1000 single channel pipette is on the left or right mount.\n", + "description": "This protocol preps a 96 well plate with Covid-19 saliva samples in up to 7 tube racks. Delays are inserted after aspiration to ensure the full volume of sample is achieved, as well as giving the user the ability to manipulate aspiration and dispense speeds.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples for this run.\n Delay After Aspiration (seconds): Specify the number of seconds after aspirating Covid sample to allow time for the full volume to be achieved.\n Aspiration/Dispense Speed: Specify the speed at which to aspirate/dispense Covid sample. A value of 1 is the default speed, a value of 0.5 is half of the default speed, etc.\n P1000 Single GEN2 Mount: Specify whether the P1000 single channel pipette is on the left or right mount.\n", "internal": "00bbd7", "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 1000uL Tips\n", "markdown": { diff --git a/protoBuilds/010526/README.json b/protoBuilds/010526/README.json index 2ded7fd58..6f4235052 100644 --- a/protoBuilds/010526/README.json +++ b/protoBuilds/010526/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: If you set Samples Labware Type to 1x 96 Well PCR Plate only a 96 Well PCR plate should be placed in Slot 2.", - "description": "This protocol performs restriction digests on a multitude of samples using various restriction enzymes and then performs an incubation on the thermocycler module for heat inactivation. The sample data is inserted using a CSV file which contains the necessary data to load enzymes, transfer reagents and location details. An example of the CSV file can be downloaded here.\nExplanation of complex parameters below:\n* P20 Single Channel GEN2 Mount Position: The position your pipette is mounted on the OT-2 (Left or Right).\n* P300 Single Channel GEN2 Mount Position: The position your pipette is mounted on the OT-2 (Left or Right).\n* Samples Labware Type: The type of labware used to hold your samples. You have the option to use 2x 24-well tuberacks (Slot 2 and 4) OR 1x 96-well NEST 100 uL PCR Plate (Slot 2).\n* Input CSV File: The input CSV file containing your sample data. You can download an example CSV file here or use the following formatting:\nUID,ng/ul,800ng (ul),Water (ul),Enzyme,Location\n1301-1,328,2,33,EcoRI,A1\n1301-2,250,3,32,EcoRI,A2\n1301-3,180,4,31,EcoRI,A3\n1303-1,145,6,29,EcoRI,A4\n1303-2,169,5,30,EcoRI,A5\n1303-3,162,5,30,EcoRI,A6\n1362-1,150,5,30,BamHI; HindIII,A7\n1362-2,156,5,30,BamHI; HindIII,A8\n1362-3,231,3,32,BamHI; HindIII,A9\n1368-1,67,12,23,BamHI; HindIII,A10\n1368-2,183,4,31,BamHI; HindIII,A11\n1368-3,231,3,32,BamHI; HindIII,A12\n* Temperature Module Hold Temperature (C): The temperature the temperature module should reach and hold to keep reagents cool. \n* Reaction Volume (uL): Total reaction volume for all samples in microliters (uL).\n* Enzyme Volume (uL): The enzyme volume used for individual enzyme transfers to the sample wells in microliters (uL).\n* Enzyme Transfer Aspirate Flow Rate (uL/s): The aspirate flow rate for the enzyme transfer step in microliters/second (uL/s).\n* Enzyme Transfer Dispense Flow Rate (uL/s): The dispense flow rate for the enzyme transfer step in microliters/second (uL/s).\n* Digest Duration (s): The total duration in seconds for the incubation at 37\u00b0C.\n* Heat Kill Temperature (\u00b0C): The temperature for heat inactivation (default: 65\u00b0C).\n* Heat Kill Duration (s): The duration in seconds for heat kill (default: 1200).\n", + "description": "This protocol performs restriction digests on a multitude of samples using various restriction enzymes and then performs an incubation on the thermocycler module for heat inactivation. The sample data is inserted using a CSV file which contains the necessary data to load enzymes, transfer reagents and location details. An example of the CSV file can be downloaded here.\nExplanation of complex parameters below:\n P20 Single Channel GEN2 Mount Position: The position your pipette is mounted on the OT-2 (Left or Right).\n P300 Single Channel GEN2 Mount Position: The position your pipette is mounted on the OT-2 (Left or Right).\n Samples Labware Type: The type of labware used to hold your samples. You have the option to use 2x 24-well tuberacks (Slot 2 and 4) OR 1x 96-well NEST 100 uL PCR Plate (Slot 2).\n Input CSV File: The input CSV file containing your sample data. You can download an example CSV file here or use the following formatting:\nUID,ng/ul,800ng (ul),Water (ul),Enzyme,Location\n1301-1,328,2,33,EcoRI,A1\n1301-2,250,3,32,EcoRI,A2\n1301-3,180,4,31,EcoRI,A3\n1303-1,145,6,29,EcoRI,A4\n1303-2,169,5,30,EcoRI,A5\n1303-3,162,5,30,EcoRI,A6\n1362-1,150,5,30,BamHI; HindIII,A7\n1362-2,156,5,30,BamHI; HindIII,A8\n1362-3,231,3,32,BamHI; HindIII,A9\n1368-1,67,12,23,BamHI; HindIII,A10\n1368-2,183,4,31,BamHI; HindIII,A11\n1368-3,231,3,32,BamHI; HindIII,A12\n Temperature Module Hold Temperature (C): The temperature the temperature module should reach and hold to keep reagents cool. \n Reaction Volume (uL): Total reaction volume for all samples in microliters (uL).\n Enzyme Volume (uL): The enzyme volume used for individual enzyme transfers to the sample wells in microliters (uL).\n Enzyme Transfer Aspirate Flow Rate (uL/s): The aspirate flow rate for the enzyme transfer step in microliters/second (uL/s).\n Enzyme Transfer Dispense Flow Rate (uL/s): The dispense flow rate for the enzyme transfer step in microliters/second (uL/s).\n Digest Duration (s): The total duration in seconds for the incubation at 37\u00b0C.\n Heat Kill Temperature (\u00b0C): The temperature for heat inactivation (default: 65\u00b0C).\n Heat Kill Duration (s): The duration in seconds for heat kill (default: 1200).\n", "internal": "010526", "labware": "\n4-in-1 Tube Rack Set\nAluminum Block Set\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons Pipette Tips\n", "markdown": { diff --git a/protoBuilds/017860/README.json b/protoBuilds/017860/README.json index 355ec3887..97616a5ef 100644 --- a/protoBuilds/017860/README.json +++ b/protoBuilds/017860/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSlots:\n1. Nunc 96 well plate 1\n2. Nunc 96 well plate 2 (optional)\n3. Nunc 96 well plate 3 (optional)\n4. Nunc 96 well plate 4 (optional)\n5. Nunc 96 well plate 5 (optional)\n6. Nunc 96 well plate 6 (optional)\n7. Tuberack with 15 mL tubes antibiotic tuberack (#2)\n8. Tuberack 4x50 mL/6x15 mL tubes - Media and antibiotics (#3)\n9. Tuberack with 15 mL tubes antibiotic tuberack (#1)\n10. 20 \u00b5l tiprack\n11. 300 \u00b5L tiprack", - "description": "This is an OT-2 compatible protocol that first transfers media and then up to 35 different antibiotics plus a barcoding dye to the wells of one to six 96 well plates based on an input CSV file. If there are more entries once the plate(s) have been filled the user is asked to replace the plates with fresh ones, as well as used tips, and the process continues until all rows of the input file have been processed.\nEach line in the csv corresponds to the transfers to a well on the plates. The plates are ordered sequentially from slot 1 to slot 6 meaning that the first 96 rows of the csv (excluding the header) correspond to the 96 wells on plate 1, and so on.\nExplanation of protocol parameters:\n* input .csv file: Here you should upload a .csv file formatted in the following way, being sure to include the header line: The first column is an identifier and is discarded by the protocol (but must be included in order for the file to be processed correctly), the 2nd column is the transfer volume of M9 media that is stored in 3 50 mL tubes on the tuberack on slot 8. The remaining columns up to n-1 are antibiotics stored on 15 mL tuberack 1 and 2 (see below). The nth column is the volume of barcoding dye.\n,M9,antibiotic 1, antibiotic 2, ... , antibiotic n, barcoding dye\n99999,50,0,0,...,0,50\n100,90,10,0,...,0,0\n* 20 uL pipette tips: Brand of pipette tips, either Opentrons or BrandTech 20 uL tips\n* 300 uL pipette tips: Brand of pipette tips, either Opentrons or BrandTech 300 uL tips\n* Number of plates: The number of Nunc 96 well plates on the deck per run, may range from one to six\n* Height offset for dispensing antibiotics into target wells [mm]: Offset for dispensing antibiotics into wells in mm (above the original level which was the calculated liquid level in the well minus 0.4 mm).\n", + "description": "This is an OT-2 compatible protocol that first transfers media and then up to 35 different antibiotics plus a barcoding dye to the wells of one to six 96 well plates based on an input CSV file. If there are more entries once the plate(s) have been filled the user is asked to replace the plates with fresh ones, as well as used tips, and the process continues until all rows of the input file have been processed.\nEach line in the csv corresponds to the transfers to a well on the plates. The plates are ordered sequentially from slot 1 to slot 6 meaning that the first 96 rows of the csv (excluding the header) correspond to the 96 wells on plate 1, and so on.\nExplanation of protocol parameters:\n input .csv file: Here you should upload a .csv file formatted in the following way, being sure to include the header line: The first column is an identifier and is discarded by the protocol (but must be included in order for the file to be processed correctly), the 2nd column is the transfer volume of M9 media that is stored in 3 50 mL tubes on the tuberack on slot 8. The remaining columns up to n-1 are antibiotics stored on 15 mL tuberack 1 and 2 (see below). The nth column is the volume of barcoding dye.\n,M9,antibiotic 1, antibiotic 2, ... , antibiotic n, barcoding dye\n99999,50,0,0,...,0,50\n100,90,10,0,...,0,0\n 20 uL pipette tips: Brand of pipette tips, either Opentrons or BrandTech 20 uL tips\n 300 uL pipette tips: Brand of pipette tips, either Opentrons or BrandTech 300 uL tips\n Number of plates: The number of Nunc 96 well plates on the deck per run, may range from one to six\n* Height offset for dispensing antibiotics into target wells [mm]: Offset for dispensing antibiotics into wells in mm (above the original level which was the calculated liquid level in the well minus 0.4 mm).\n", "internal": "017860", "labware": "\nOpentrons 20 uL tipracks\n300 uL tipracks\nBrandTech 20 uL tipracks\nBrandTech 300 uL tipracks\nNunc 400 \u00b5L 96 well plate\nOpentrons tuberacks\nOpentrons tubes\nFalcon tubes\n", "markdown": { diff --git a/protoBuilds/019a7d_part_2/README.json b/protoBuilds/019a7d_part_2/README.json index 0d2eb8d44..d1df5c413 100644 --- a/protoBuilds/019a7d_part_2/README.json +++ b/protoBuilds/019a7d_part_2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck Layout, temp modules should initially be set to 4 C in both slot 1 and 4\n\n", - "description": "This is part 2 of a 2 part protocol for prepping then loading nucleic acid onto agar plates. It requires both a multichannel and single channel 20ul pipette.\nPart one can be found here\nThe basic outline follows:\nThe assembly plate liquid is added to a Mix and Go plate. A heat shock can be performed, bringing the Mix and Go plate to 42 C for 40 seconds then back to the holding temperature of 4 C. After 30 minutes, agar plates are loaded with the resultant mixture as specified in the parameters. If desired, this Mix and Go plate's liquid can be added to a deep well plate and mixed with liquid culture.\nTips are reused for the same sample repeatedly, i.e. sample A1 on the Mix and Go will use A1 in the tip rack.\nExplanation of complex parameters below:\n* Number of Samples: Number of samples in Mix and Go plate. Can be any number between 1 and 96\n* 24 or 96 Distributions per Plate: Choose to use up to four agar plates with 24 samples each and/or one agar plate with up to 96 samples. Distribution of samples follows a common layout for either 24 well plates or 96 well plates on the agar\n* Heat Shock: Choose yes or no to determine whether a heat shock will occur during the protocol. This heat shock takes place after adding to the Mix and Go plate. It raises the temperature to 42 C for 40 seconds before returning to 4 C\n* Volume to Distribute on Agar: Choose a liquid volume to add to the agar plate(s). This can theoretically be many volumes above 1 ul but caution should be exercised so as not to co-mingle samples on the agar by overloading\n* Add to Deep Well Plate: Choose yes or no to add to deep well plate. Yes results in a specified amount of liquid being added to the deep well plate 1 cm above the well bottom and mixed\n* Volume to Add to Deep Well Plate: Specifies volume to add to the deep well plate if yes is chosen under \"Add to Deep Well Plate\"\n", + "description": "This is part 2 of a 2 part protocol for prepping then loading nucleic acid onto agar plates. It requires both a multichannel and single channel 20ul pipette.\nPart one can be found here\nThe basic outline follows:\nThe assembly plate liquid is added to a Mix and Go plate. A heat shock can be performed, bringing the Mix and Go plate to 42 C for 40 seconds then back to the holding temperature of 4 C. After 30 minutes, agar plates are loaded with the resultant mixture as specified in the parameters. If desired, this Mix and Go plate's liquid can be added to a deep well plate and mixed with liquid culture.\nTips are reused for the same sample repeatedly, i.e. sample A1 on the Mix and Go will use A1 in the tip rack.\nExplanation of complex parameters below:\n Number of Samples: Number of samples in Mix and Go plate. Can be any number between 1 and 96\n 24 or 96 Distributions per Plate: Choose to use up to four agar plates with 24 samples each and/or one agar plate with up to 96 samples. Distribution of samples follows a common layout for either 24 well plates or 96 well plates on the agar\n Heat Shock: Choose yes or no to determine whether a heat shock will occur during the protocol. This heat shock takes place after adding to the Mix and Go plate. It raises the temperature to 42 C for 40 seconds before returning to 4 C\n Volume to Distribute on Agar: Choose a liquid volume to add to the agar plate(s). This can theoretically be many volumes above 1 ul but caution should be exercised so as not to co-mingle samples on the agar by overloading\n Add to Deep Well Plate: Choose yes or no to add to deep well plate. Yes results in a specified amount of liquid being added to the deep well plate 1 cm above the well bottom and mixed\n Volume to Add to Deep Well Plate: Specifies volume to add to the deep well plate if yes is chosen under \"Add to Deep Well Plate\"\n", "internal": "019a7d", "labware": "\n2x Azenta Life Sciences 96 Well Plate, 200 ul\n1x Greiner 96 Deep Well Plate, 2 ml\n5x Thermo Fisher Omni Nunc Tray\n1x Opentrons 20ul Filter Tip Racks\n", "markdown": { diff --git a/protoBuilds/022548-2/README.json b/protoBuilds/022548-2/README.json index 60a932382..2bdb728e4 100644 --- a/protoBuilds/022548-2/README.json +++ b/protoBuilds/022548-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nLoad 300 ul tip racks in order 6-3. Load tube racks in order from top down. Load samples in order down the column in each tube rack. Tube racks should be filled fully before proceeding to next tube rack. For example, 33 samples total would mean 32 in the top most tube rack and 1 sample in the middle tube rack.\n\n", - "description": "This protocol transfers samples from tubes in up to 3 PRL tuberacks to a destination plate followed by resuspending a bead/binding buffer mastermix before transfering it to the samples on the plate.\nLinks:\n* Part 1: Master Mix Assembly\n* Part 2: Master Mix Distribution and Sample Transfer\nExplanation of parameters below:\n* Number of samples in tuberack 1 slot 10-11: How many samples to transfer from rack 1: 1 to 32\n* Number of samples in tuberack 2 slot 7-8: 0 to 32\n* Number of samples in tuberack 3 slot 4-5: 0 to 32\n* Master mix wells location: Informs the protocol which wells of the reservoir contain mastermix, starting from A1 on the very left. For example 1-4 to specify wells A1 to A4. This parameter may also be a single number instead of a range\n* Mastermix max volume per well (mL): Informs the protocol what the maximal volume of mastermix is in each reservoir well, default is 9.54 mL\n* Mastermix mixing rate multiplier: Controls the flow rate of mixing, 1.0 means standard flow rate, less is slower and more is faster.\n* mastermix aspiration flow rate multiplier: Controls the rate of aspiration of mastermix from the reservoir wells\n* mastermix dispension flow rate multiplier: Controls the rate of dispension of mastermix into wells on the target plate\n* Mount for 300 uL single channel pipette: Left or right\n* Mount for 300 uL multi channel pipette: Left or right\n* Pause after mixing the mastermix for vortex/resuspension?: Optional pause after (re-)mixing the mastermix where the reservoir may be taken out for manual resuspension such as vortexing, nutation or shaking if resuspension by pipetting is deemed insufficient.\n", + "description": "This protocol transfers samples from tubes in up to 3 PRL tuberacks to a destination plate followed by resuspending a bead/binding buffer mastermix before transfering it to the samples on the plate.\nLinks:\n Part 1: Master Mix Assembly\n Part 2: Master Mix Distribution and Sample Transfer\nExplanation of parameters below:\n Number of samples in tuberack 1 slot 10-11: How many samples to transfer from rack 1: 1 to 32\n Number of samples in tuberack 2 slot 7-8: 0 to 32\n Number of samples in tuberack 3 slot 4-5: 0 to 32\n Master mix wells location: Informs the protocol which wells of the reservoir contain mastermix, starting from A1 on the very left. For example 1-4 to specify wells A1 to A4. This parameter may also be a single number instead of a range\n Mastermix max volume per well (mL): Informs the protocol what the maximal volume of mastermix is in each reservoir well, default is 9.54 mL\n Mastermix mixing rate multiplier: Controls the flow rate of mixing, 1.0 means standard flow rate, less is slower and more is faster.\n mastermix aspiration flow rate multiplier: Controls the rate of aspiration of mastermix from the reservoir wells\n mastermix dispension flow rate multiplier: Controls the rate of dispension of mastermix into wells on the target plate\n Mount for 300 uL single channel pipette: Left or right\n Mount for 300 uL multi channel pipette: Left or right\n* Pause after mixing the mastermix for vortex/resuspension?: Optional pause after (re-)mixing the mastermix where the reservoir may be taken out for manual resuspension such as vortexing, nutation or shaking if resuspension by pipetting is deemed insufficient.\n", "internal": "022548-2", "labware": "\nNEST 12-Well Reservoirs, 15 mL\nPRL tuberack for 32 15 mL tubes\nThermo Fisher Kingfisher 96 deepwell plate 2 mL\n", "markdown": { diff --git a/protoBuilds/022548/README.json b/protoBuilds/022548/README.json index 549ab90df..41759ca34 100644 --- a/protoBuilds/022548/README.json +++ b/protoBuilds/022548/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol create a mastermix of binding buffer and bead mix. For large volumes the deck should use a NEST 12 well reservoir for the bead mix, for smaller number of samples a tuberack may be used as source for bead mix.\nDesignate the wells used for binding buffer and bead mix and the mastermix is created starting in the well immediately after, and uses as many wells as required for creating mastermix for the indicated number of samples. The protocol creates a dead volume in addition to the 'active' volume of mastermix (1 mL for reservoirs) - this is to avoid the pipette aspirating air during mastermix dispension in part 2 of the protocol.\nThe protocol will create a maximum volume of 9.54 mL per well, of which 1/3rd is dead volume.\nThe protocol is written to account for the changing liquid level of bead source tubes so that the pipette will not plunge too far into tube solutions.\nLinks:\n* Part 1: Master Mix Assembly\n* Part 2: Master Mix Distribution and Sample Transfer\nExplanation of parameters below:\n* Create mastermix for how many numbers of samples: How many samples to create mastermix for.\n* Binding buffer wells: Designates which wells contain binding buffer, you may specify a range such as 1-4, or a single number if it is a single well. These number corresponds to the wells of the reservoir starting at the leftmost well.\n* Bead mix well(s): Which well(s) contain bead mix. Just like the previous parameter it can be a number or a range, e.g. 5, or 5-6\n* Volume of binding buffer per source well (mL): How many milliliters of binding buffer is contained in each source reservoir well.\n* Volume of bead mix per source well (mL): How many milliliters of bead mix is contained in the source tube/reservoir well(s)\n* P300 single channel pipette mount: Left or right mount\n* P300 multi channel pipette mount: Left or right mount\n* Mastermix tuberack (Optional, only for small volumes of mastermix): Specify what kind of tuberack contains your bead mix tube. If this parameter is set to none the bead source will be a NEST 12 well reservoir instead (default).\n* Mastermix mixing rate multiplier: The multiplier scales the flow rate of mixing aspirations and dispenses, e.g. 1.0 is the standard mixing rate, 0.5 would be half etc.\n* Binding buffer aspiration flow rate multiplier: Controls the flow rate of aspiration when aspirating binding buffer from a source well\n* Binding buffer dispensing flow rate multiplier: Controls the flow rate of dispension when dispensing binding buffer in a mastermix target well\n* Bead solution aspiration flow rate multiplier: Controls the flow rate of aspiration when aspirating from a bread mix source well\n* Bead solution dispensing flow rate multiplier: Controls the flow rate of dispension when dispensing bead mix in a mastermix target well\n* How many times do you want to mix the mastermix?: Indicates the number of times you want to mix the mastermix solution after the binding buffer and bead mix have been added.\n* Mastermix mixing rate multiplier: flow-rate modifier affecting the rate of aspiration and dispensing for mixing the mastermix after the addition of both components.\n* Offsets from the edges of the reservoir wells for bead mix dispenses (mm): Offset defining how close the pipette may get to the edge of the reservoir well when dispensing bead mix into the mastermix wells (which is dispensed in three different locations inside of the well)\n* Verbose protocol output?: Indicates to the protocol whether it should output extra information about what it is doing.\n", + "description": "This protocol create a mastermix of binding buffer and bead mix. For large volumes the deck should use a NEST 12 well reservoir for the bead mix, for smaller number of samples a tuberack may be used as source for bead mix.\nDesignate the wells used for binding buffer and bead mix and the mastermix is created starting in the well immediately after, and uses as many wells as required for creating mastermix for the indicated number of samples. The protocol creates a dead volume in addition to the 'active' volume of mastermix (1 mL for reservoirs) - this is to avoid the pipette aspirating air during mastermix dispension in part 2 of the protocol.\nThe protocol will create a maximum volume of 9.54 mL per well, of which 1/3rd is dead volume.\nThe protocol is written to account for the changing liquid level of bead source tubes so that the pipette will not plunge too far into tube solutions.\nLinks:\n Part 1: Master Mix Assembly\n Part 2: Master Mix Distribution and Sample Transfer\nExplanation of parameters below:\n Create mastermix for how many numbers of samples: How many samples to create mastermix for.\n Binding buffer wells: Designates which wells contain binding buffer, you may specify a range such as 1-4, or a single number if it is a single well. These number corresponds to the wells of the reservoir starting at the leftmost well.\n Bead mix well(s): Which well(s) contain bead mix. Just like the previous parameter it can be a number or a range, e.g. 5, or 5-6\n Volume of binding buffer per source well (mL): How many milliliters of binding buffer is contained in each source reservoir well.\n Volume of bead mix per source well (mL): How many milliliters of bead mix is contained in the source tube/reservoir well(s)\n P300 single channel pipette mount: Left or right mount\n P300 multi channel pipette mount: Left or right mount\n Mastermix tuberack (Optional, only for small volumes of mastermix): Specify what kind of tuberack contains your bead mix tube. If this parameter is set to none the bead source will be a NEST 12 well reservoir instead (default).\n Mastermix mixing rate multiplier: The multiplier scales the flow rate of mixing aspirations and dispenses, e.g. 1.0 is the standard mixing rate, 0.5 would be half etc.\n Binding buffer aspiration flow rate multiplier: Controls the flow rate of aspiration when aspirating binding buffer from a source well\n Binding buffer dispensing flow rate multiplier: Controls the flow rate of dispension when dispensing binding buffer in a mastermix target well\n Bead solution aspiration flow rate multiplier: Controls the flow rate of aspiration when aspirating from a bread mix source well\n Bead solution dispensing flow rate multiplier: Controls the flow rate of dispension when dispensing bead mix in a mastermix target well\n How many times do you want to mix the mastermix?: Indicates the number of times you want to mix the mastermix solution after the binding buffer and bead mix have been added.\n Mastermix mixing rate multiplier: flow-rate modifier affecting the rate of aspiration and dispensing for mixing the mastermix after the addition of both components.\n Offsets from the edges of the reservoir wells for bead mix dispenses (mm): Offset defining how close the pipette may get to the edge of the reservoir well when dispensing bead mix into the mastermix wells (which is dispensed in three different locations inside of the well)\n* Verbose protocol output?: Indicates to the protocol whether it should output extra information about what it is doing.\n", "internal": "022548-1", "labware": "\nNEST 12-Well Reservoirs, 15 mL\nOpentrons tuberacks\n", "markdown": { diff --git a/protoBuilds/02pnzp/README.json b/protoBuilds/02pnzp/README.json index 9b995acc1..e6e5a016f 100644 --- a/protoBuilds/02pnzp/README.json +++ b/protoBuilds/02pnzp/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "deck", - "description": "This protocol will prepare and run a standard Endpoint-PCR with the opentrons Cycler Module (only tested with Gen1). It aims to provide sufficient flexibility in terms of sample and replicate numbers to avoid the need of multiple similar protocols.\nKey benefits of the protocol are:\n* The master mixes will be prepared in 50 ml falcons and all reagents and samples can be provided in 1.5 ml tubes.\n* Thus, no manual pipetting steps are involved.\n* Up to 12 different template samples can be used with up to 3 different master mixes.\n* Only the p300 and p20 pipettes are needed.\n* Needed volumes of the different reagents are calculated and shown in run tab.\nNotes:\n* A no-template control (NTC) will be automatically added for each master mix.\n* The first well of every master mix will always be in row A. If the sample number + NTC is not a multiple of 8, the remaining wells of the last column will be left empty to have an easier plate layout.\n* (e.g. You have 2 master mixes, 4 samples and 1 replicate each. The last well of master mix 1 will be E1 (NTC control). Master mix 2 will now be added to the wells A2 - E2, skipping the remaining wells of column 1. This is meant to make it less confusing down the road.)", + "description": "This protocol will prepare and run a standard Endpoint-PCR with the opentrons Cycler Module (only tested with Gen1). It aims to provide sufficient flexibility in terms of sample and replicate numbers to avoid the need of multiple similar protocols.\nKey benefits of the protocol are:\n The master mixes will be prepared in 50 ml falcons and all reagents and samples can be provided in 1.5 ml tubes.\n Thus, no manual pipetting steps are involved.\n Up to 12 different template samples can be used with up to 3 different master mixes.\n Only the p300 and p20 pipettes are needed.\n* Needed volumes of the different reagents are calculated and shown in run tab.\nNotes:\n A no-template control (NTC) will be automatically added for each master mix.\n The first well of every master mix will always be in row A. If the sample number + NTC is not a multiple of 8, the remaining wells of the last column will be left empty to have an easier plate layout.\n* (e.g. You have 2 master mixes, 4 samples and 1 replicate each. The last well of master mix 1 will be E1 (NTC control). Master mix 2 will now be added to the wells A2 - E2, skipping the remaining wells of column 1. This is meant to make it less confusing down the road.)", "internal": "02pnzp", "labware": "\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 24 Well Aluminum Block with NEST 1.5 mL Screwcap\nOpentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap\nOpentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L\nOpentrons 10 Tube Rack with Falcon 4x50 mL, 6x15 mL Conical\n", "markdown": { diff --git a/protoBuilds/04eeb1-part-2/README.json b/protoBuilds/04eeb1-part-2/README.json index 4a07bf4ee..23d73ee20 100644 --- a/protoBuilds/04eeb1-part-2/README.json +++ b/protoBuilds/04eeb1-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: Master Mix should be added in Column 2 (A2) of any reservoir type.\n", - "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the second part of a seven part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n* P20 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n* Reservoir Labware Type: Choose the type of reservoir that will be used for holding the master mix. Note: Only the Bio-Rad Hard-Shell 96 Well Plate 200 \u00b5L plate will resume after Plate 1 and prompt for a refill of the master mix.\n* Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n", + "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the second part of a seven part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n P20 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n Reservoir Labware Type: Choose the type of reservoir that will be used for holding the master mix. Note: Only the Bio-Rad Hard-Shell 96 Well Plate 200 \u00b5L plate will resume after Plate 1 and prompt for a refill of the master mix.\n Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n", "internal": "04eeb1-part-2", "labware": "\nOpentrons 20 uL Filter Tips\nBio-Rad Hard-Shell 96 Well Plate 200 \u00b5L PCR\nNEST 2 mL 96-Well Deep Well Plate\nNEST 12-Well Reservoirs, 15 mL\n", "markdown": { diff --git a/protoBuilds/04eeb1-part-3/README.json b/protoBuilds/04eeb1-part-3/README.json index 46c0029c6..c1f606be5 100644 --- a/protoBuilds/04eeb1-part-3/README.json +++ b/protoBuilds/04eeb1-part-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the third part of a seven part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n* P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n* Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n* Plate 1 Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n* Plate 2 Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 2.\n", + "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the third part of a seven part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n Plate 1 Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n Plate 2 Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 2.\n", "internal": "04eeb1-part-3", "labware": "\nOpentrons 200 uL Filter Tips\nBio-Rad Hard-Shell 96 Well Plate 200 \u00b5L PCR\nNEST 12-Well Reservoirs, 15 mL\n", "markdown": { diff --git a/protoBuilds/04eeb1-part-4/README.json b/protoBuilds/04eeb1-part-4/README.json index e64bd84a9..6b5f3fcf8 100644 --- a/protoBuilds/04eeb1-part-4/README.json +++ b/protoBuilds/04eeb1-part-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the fourth part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n* P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n* Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n* Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n", + "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the fourth part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n* Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n", "internal": "04eeb1-part-4", "labware": "\nOpentrons 200 uL Filter Tips\nBio-Rad Hard-Shell 96 Well Plate 200 \u00b5L PCR\nNEST 12-Well Reservoirs, 15 mL\n", "markdown": { diff --git a/protoBuilds/04eeb1-part-5/README.json b/protoBuilds/04eeb1-part-5/README.json index e38bde86c..56dcac879 100644 --- a/protoBuilds/04eeb1-part-5/README.json +++ b/protoBuilds/04eeb1-part-5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: Wash Buffer should be added in Column 2 (A2).\n", - "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the fifth part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n* P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n* Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n* Wash Buffer Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n", + "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the fifth part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n Wash Buffer Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n", "internal": "04eeb1-part-5", "labware": "\nOpentrons 200 uL Filter Tips\nBio-Rad Hard-Shell 96 Well Plate 200 \u00b5L PCR\nNEST 12-Well Reservoirs, 15 mL\n", "markdown": { diff --git a/protoBuilds/04eeb1-part-6/README.json b/protoBuilds/04eeb1-part-6/README.json index b1f2e662e..3f56aec5a 100644 --- a/protoBuilds/04eeb1-part-6/README.json +++ b/protoBuilds/04eeb1-part-6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: AMP Master Mix should be added in Column 3 (A3).\n", - "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the sixth part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n* P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n* Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n* Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n", + "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the sixth part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n Master Mix Column: Choose the column on the 12-channel reservoir for the master mix for Plate 1.\n", "internal": "04eeb1-part-6", "labware": "\nOpentrons 200 uL Filter Tips\nBio-Rad Hard-Shell 96 Well Plate 200 \u00b5L PCR\nNEST 12-Well Reservoirs, 15 mL\n", "markdown": { diff --git a/protoBuilds/04eeb1-part-7/README.json b/protoBuilds/04eeb1-part-7/README.json index c0d6e6a46..fdb7ec03b 100644 --- a/protoBuilds/04eeb1-part-7/README.json +++ b/protoBuilds/04eeb1-part-7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: Add PCR strip on Column 1 of 96 Well Aluminum block in Slot 9. Add 1.7 mL tube to A1 of 24 Well Aluminum block on slot 6.\n", - "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the seventh part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n* P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n* P20 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n", + "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the seventh part of a seven-part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n P300 Multichannel GEN2 Pipette Mount: Choose the mount position of your P300 Multichannel pipette, either left or right.\n P20 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n", "internal": "04eeb1-part-7", "labware": "\nOpentrons 200 uL Filter Tips\nBio-Rad Hard-Shell 96 Well Plate 200 \u00b5L PCR\n", "markdown": { diff --git a/protoBuilds/04eeb1/README.json b/protoBuilds/04eeb1/README.json index aaa80fa22..1d6d94d49 100644 --- a/protoBuilds/04eeb1/README.json +++ b/protoBuilds/04eeb1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: Master Mix should be added in Column 1 (A1) of any reservoir type.\n", - "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the first part of a seven part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n* P20 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n* Reservoir Labware Type: Choose the type of reservoir that will be used for holding the master mix. Note: Only the Bio-Rad Hard-Shell 96 Well Plate 200 \u00b5L plate will resume after Plate 1 and prompt for a refill of the master mix.\n* Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n", + "description": "The Illumina COVIDSeq Test is a high-throughput, next-generation sequencing test that is used fo detecting SARS-CoV-2 in patient samples. This protocol is the first part of a seven part protocol that is run on the OT-2 for this kit.\n\nPart 1: Anneal RNA\nPart 2: Synthesize First Strand cDNA\nPart 3: Amplify cDNA\nPart 4: Tagment PCR Amplicons\nPart 5: Post Tagmentation Clean Up\nPart 6: Amplify Tagmented Amplicons\nPart 7: Pool and Clean Up Libraries\n\nExplanation of complex parameters below:\n P20 Multichannel GEN2 Pipette Mount: Choose the mount position of your P20 Multichannel pipette, either left or right.\n Reservoir Labware Type: Choose the type of reservoir that will be used for holding the master mix. Note: Only the Bio-Rad Hard-Shell 96 Well Plate 200 \u00b5L plate will resume after Plate 1 and prompt for a refill of the master mix.\n Plate 1 Columns: Choose which columns master mix should be added on plate 1. Separate column numbers with a comman (Ex: 1,2,3,4).\n Plate 2 Columns: Choose which columns master mix should be added on plate 2. Separate column numbers with a comman (Ex: 1,2,3,4).\n* Temperature (C): Choose the temperature the temperature module should be set at in the beginning of the protocol.\n", "internal": "04eeb1", "labware": "\nOpentrons 20 uL Filter Tips\nBio-Rad Hard-Shell 96 Well Plate 200 \u00b5L PCR\nNEST 2 mL 96-Well Deep Well Plate\nNEST 12-Well Reservoirs, 15 mL\n", "markdown": { diff --git a/protoBuilds/04f310/README.json b/protoBuilds/04f310/README.json index 12be83ba7..65721b6c1 100644 --- a/protoBuilds/04f310/README.json +++ b/protoBuilds/04f310/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons 10-Tube Rack with Falcon 50 mL Conical Tube (containing 40 mL water) \nSlot 5: BioRad 200 uL PCR Plate (output plate) \nSlot 8: BioRad 200 uL PCR Plate (intermediate dilution plate) \nSlot 9: Agilent 290 mL Reservoir (filled with 10 percent diluted bleach) \nSlot 11: NEST 96 Deep Well Plate 2 mL (containing input DNA samples >= 50 uL) \nSlot 7: Opentrons 20 uL filter tips \nSlot 10: Opentrons 200 uL filter tips \n", - "description": "This protocol uses single-channel P20 and P300 pipettes to normalize DNA concentrations of up to 96 input samples based on user input (input DNA sample concentration, target concentration, target volume) provided by csv file upload (see example file below). Intermediate dilutions are prepared as needed. A downloadable output file is generated to record calculated fold dilution, volume of sample and water transferred, if a sample was processed (or skipped due to insufficient input DNA concentration), and if an intermediate dilution was required.\nLinks:\n* example input csv\n\nValues for CSV file input:\n* sample_id\n* dna_conc_initial (ng/ul)\n* dna_conc_target (ng/ul) 5-40 ng/uL\n* volume_target (ul) 30-100 uL\n\nAdditional Calculated Values in CSV file output:\n* fold dilution\n* sample_transfer (ul)\n* water_transfer (ul)\n* processed (0 - sample was skipped, 1 - sample was processed)\n* intermediate_dilution (0 - intermediate dilution not required, 1 - intermediate dilution required)\n", + "description": "This protocol uses single-channel P20 and P300 pipettes to normalize DNA concentrations of up to 96 input samples based on user input (input DNA sample concentration, target concentration, target volume) provided by csv file upload (see example file below). Intermediate dilutions are prepared as needed. A downloadable output file is generated to record calculated fold dilution, volume of sample and water transferred, if a sample was processed (or skipped due to insufficient input DNA concentration), and if an intermediate dilution was required.\nLinks:\n* example input csv\n\nValues for CSV file input:\n sample_id\n dna_conc_initial (ng/ul)\n dna_conc_target (ng/ul) 5-40 ng/uL\n volume_target (ul) 30-100 uL\n\nAdditional Calculated Values in CSV file output:\n fold dilution\n sample_transfer (ul)\n water_transfer (ul)\n processed (0 - sample was skipped, 1 - sample was processed)\n* intermediate_dilution (0 - intermediate dilution not required, 1 - intermediate dilution required)\n", "internal": "04f310", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons 10-Tube Rack] (https://shop.opentrons.com/4-in-1-tube-rack-set/)\n[BioRad 200 uL PCR Plate] (https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr?category=wellPlate)\n[NEST 96 Deep Well Plate 2 mL] (https://labware.opentrons.com/nest_96_wellplate_2ml_deep?category=wellPlate)\n[Agilent 290 mL Reservoir] (https://labware.opentrons.com/agilent_1_reservoir_290ml?category=reservoir)\n", "markdown": { diff --git a/protoBuilds/04f4e7/README.json b/protoBuilds/04f4e7/README.json index 6e6d0cb5e..50d0c10f6 100644 --- a/protoBuilds/04f4e7/README.json +++ b/protoBuilds/04f4e7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nIf the deck layout of a particular protocol is more or less static, it is often helpful to attach a preview of the deck layout, most descriptively generated with Labware Creator. Example:\n\n", - "description": "This protocol performs an RNA extraction on a user-specified number of samples. Beads are pre-mixed and added to sample with 5 sequential incubation-mix periods. Excess liquid is picked off the top of the wells and dispensed into waste, and the remaining liquid + beads are added to the magnetic plate. After two PBS washes, elution and neutralization buffer are added to the samples. Samples are then moved to the elution plate, with beads in the mag plate collected for later use. \nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples to be processed this run.\n* Slow Aspiration Rate (Step 7): Specify the aspiration rate for Step 7 in the protocol. A value of 1 is the default flow rate, a value of 0.5 would be half of the default flow rate, and so on.\n* Aspiration Height to Remove Top Liquid (Step 7): Specify the aspiration height to aspirate 3 X 300ul from as specified in Step 7 in the protocol.\n* Aspiration Height to Remove Supernatant: Specify the aspiration height to remove supernatant from.\n* Incubation Time After Engaging Magnet: Specify the incubation time after engaging the magnet (in minutes).\n* Length From Side of Well Opposite Magnetically Engaged Beads: Specify the distance from the side of the well opposite magnetically engaged beads to aspirate from. A value of 2 is 2mm from the side of the well opposite magnetically engaged beads.\n* P300 Multi-Channel Mount: Specify which mount (left or right) for the P300 multi-channel pipette.\n", + "description": "This protocol performs an RNA extraction on a user-specified number of samples. Beads are pre-mixed and added to sample with 5 sequential incubation-mix periods. Excess liquid is picked off the top of the wells and dispensed into waste, and the remaining liquid + beads are added to the magnetic plate. After two PBS washes, elution and neutralization buffer are added to the samples. Samples are then moved to the elution plate, with beads in the mag plate collected for later use. \nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples to be processed this run.\n Slow Aspiration Rate (Step 7): Specify the aspiration rate for Step 7 in the protocol. A value of 1 is the default flow rate, a value of 0.5 would be half of the default flow rate, and so on.\n Aspiration Height to Remove Top Liquid (Step 7): Specify the aspiration height to aspirate 3 X 300ul from as specified in Step 7 in the protocol.\n Aspiration Height to Remove Supernatant: Specify the aspiration height to remove supernatant from.\n Incubation Time After Engaging Magnet: Specify the incubation time after engaging the magnet (in minutes).\n Length From Side of Well Opposite Magnetically Engaged Beads: Specify the distance from the side of the well opposite magnetically engaged beads to aspirate from. A value of 2 is 2mm from the side of the well opposite magnetically engaged beads.\n* P300 Multi-Channel Mount: Specify which mount (left or right) for the P300 multi-channel pipette.\n", "internal": "04f4e7", "labware": "\nNunc\u2122 96-Well Polypropylene DeepWell\u2122 Storage Plates 278743\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNest 1 well Reservoir 195mL\nNest 12 well Reservoir 15mL\nOpentrons 300ul tips\n", "markdown": { diff --git a/protoBuilds/055b94/README.json b/protoBuilds/055b94/README.json index d9ece80d3..0e728bd60 100644 --- a/protoBuilds/055b94/README.json +++ b/protoBuilds/055b94/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "deck-setup": "\n* yellow on 96-wellplates: sample\n* blue on tuberack: prepared mastermix\n* purple on strips: mastermix strips for plating (loaded empty)", + "deck-setup": "\n yellow on 96-wellplates: sample\n blue on tuberack: prepared mastermix\n* purple on strips: mastermix strips for plating (loaded empty)", "description": "This protocol provides a custom qPCR prep on the OT-2 for up to 4x source 96-well plates into 1x destination 384-wellplate. Mastermix is prepared manually and transferred to each reaction well on the OT-2.\nEach protocol run generates an output .csv file that is compatible with Quantstudio instruments. To retrieve the file, launch a Jupyter Notebook server on your robot by following these instructions. The file will be named after the 9000 plate barcode scan, followed by \".csv.\"", "internal": "055b94", "labware": "\nKingFisher 96 Well Plate 200 \u00b5L #97002540\nThermoFisher Microamp 96 Aluminum Block 200 \u00b5L #4346906\nMicroamp 384 Well Plate 40 \u00b5L #4483273\ncustom 24 Tube Rack with Custom 2 mL\nKingFisher 96 Deep Well Plate #95040450\nCustom 96 Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n", diff --git a/protoBuilds/059126/README.json b/protoBuilds/059126/README.json index bdb8af957..0283514b9 100644 --- a/protoBuilds/059126/README.json +++ b/protoBuilds/059126/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nStarting Deck Setup for 2 Reagent Vials:\n\n\n", - "description": "This is a specialized reagent addition to add reagent from vials in a Cytiva well plate to a 96 well plate which are then transferred to a 384 well plate. The vials and transfer volumes are specified via a CSV file. The tips are picked up in a non-standard manner with a single tip picked up from the bottom of a specified column continuing up and to the left with each new tip pick-up. E.g. Column 11 is specified, first tip picked up will be H11, then G11, F11,.....H10, G10, etc. These single tips are used to add from the vials to the 96 well plate. The columns of the 96 well plate will then have a specified amount of each column added to the 384 well plate, reusing tips as much as possible. Transfer volumes from the vials to the 96 well plate, transfer volumes from the 96 well plate to the 384 well plate, and which vials will be used is specified by uploading a CSV. The specific format can be found in this example CSV located here\nExplanation of complex parameters below:\n* Number of Columns in 384 Well Plate: How many columns will be in the 384 well plate starting from the left side\n* Starting Tip Column (1-12): Which tip will be picked up first. Number corresponds to column from left to right. Bottom tip will be picked up first in each column.\n* P20 Multi GEN2 Mount: Which mount the P20 multi-channel is connected to. The P300 will be connected to the opposite mount.\n* Transfer .CSV File: Upload the CSV file with vial list and transfer volumes.\n", + "description": "This is a specialized reagent addition to add reagent from vials in a Cytiva well plate to a 96 well plate which are then transferred to a 384 well plate. The vials and transfer volumes are specified via a CSV file. The tips are picked up in a non-standard manner with a single tip picked up from the bottom of a specified column continuing up and to the left with each new tip pick-up. E.g. Column 11 is specified, first tip picked up will be H11, then G11, F11,.....H10, G10, etc. These single tips are used to add from the vials to the 96 well plate. The columns of the 96 well plate will then have a specified amount of each column added to the 384 well plate, reusing tips as much as possible. Transfer volumes from the vials to the 96 well plate, transfer volumes from the 96 well plate to the 384 well plate, and which vials will be used is specified by uploading a CSV. The specific format can be found in this example CSV located here\nExplanation of complex parameters below:\n Number of Columns in 384 Well Plate: How many columns will be in the 384 well plate starting from the left side\n Starting Tip Column (1-12): Which tip will be picked up first. Number corresponds to column from left to right. Bottom tip will be picked up first in each column.\n P20 Multi GEN2 Mount: Which mount the P20 multi-channel is connected to. The P300 will be connected to the opposite mount.\n Transfer .CSV File: Upload the CSV file with vial list and transfer volumes.\n", "internal": "059126", "labware": "\nGreiner 96 Well Plate 340uL\nGreiner 384 Well Plate 50uL\nCytive 24 Well Plate 2000uL used as Vial Holder\n", "markdown": { diff --git a/protoBuilds/05f673/README.json b/protoBuilds/05f673/README.json index 35647088a..4a8ce2ce2 100644 --- a/protoBuilds/05f673/README.json +++ b/protoBuilds/05f673/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Source plates containing samples can be placed in deck slots 1, 2, 3, and 5 (and should be referred to as 1-4 in the CSV). Destination plates (where buffer and cells will be added) can be placed in deck slots 6, 8, 9, and 11 (and should be referred to as 1-4 in the CSV). Tips should be placed in deck slot 7.\n", - "description": "This protocol allows for a robust cherrypicking and normalization in one step.\n\nUsing a P1000 Single-Channel Pipette, buffer will be transferred to all wells specified in the Normalization CSV (see below), before transferring samples from up to four source plates to four destination plates (specific plate and well location specifed in Normalization CSV).\n\nThe .csv file should be formatted as shown in the example below, including headers:\nSource Plate, Source Well, Dest Plate, Dest Well, Buffer Volume (in ul), Culture Volume (in ul)\n2,A1,1,A1,1591,1870\n2,B1,2,B1,1629,808\n\nUpdate: This protocol has been updated per user request and now allows for the option to use 96-well plates and (if using 96-well plates), prefill the plates with a P300 8-Channel Pipette.\nExplanation of complex parameters below:\n* P1000 (GEN2) Mount: Specify whether the P1000 single channel pipette is on the left or right mount.\n* Normalization CSV: CSV containing transfer information for normalization (as outlined above).\n* Labware Type: Select between Corning 24-Well Plate and Corning 96-Well Plate.\n* Prefill Volume: Specify the volume (in \u00b5L) to prefill the 96-Well plates.\n", + "description": "This protocol allows for a robust cherrypicking and normalization in one step.\n\nUsing a P1000 Single-Channel Pipette, buffer will be transferred to all wells specified in the Normalization CSV (see below), before transferring samples from up to four source plates to four destination plates (specific plate and well location specifed in Normalization CSV).\n\nThe .csv file should be formatted as shown in the example below, including headers:\nSource Plate, Source Well, Dest Plate, Dest Well, Buffer Volume (in ul), Culture Volume (in ul)\n2,A1,1,A1,1591,1870\n2,B1,2,B1,1629,808\n\nUpdate: This protocol has been updated per user request and now allows for the option to use 96-well plates and (if using 96-well plates), prefill the plates with a P300 8-Channel Pipette.\nExplanation of complex parameters below:\n P1000 (GEN2) Mount: Specify whether the P1000 single channel pipette is on the left or right mount.\n Normalization CSV: CSV containing transfer information for normalization (as outlined above).\n Labware Type: Select between Corning 24-Well Plate and Corning 96-Well Plate.\n Prefill Volume: Specify the volume (in \u00b5L) to prefill the 96-Well plates.\n", "internal": "05f673", "labware": "Corning 24-Well Plate, 3.4mL, Flat or Corning 96-Well Plate, 360\u00b5L, Flat\nAgilent 1-Well Reservoir, 290mL\nOpentrons 1000uL Tips\nOpentrons 300uL Tips, optional", "markdown": { diff --git a/protoBuilds/060c4f/README.json b/protoBuilds/060c4f/README.json index d52892b54..f38202187 100644 --- a/protoBuilds/060c4f/README.json +++ b/protoBuilds/060c4f/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol automates the distribution of samples from a 96-well plate (on the Temperature Module) to a 384-well plate.\n\nGiven the mapping differences between a 96-well plate and a 384-well plate, the user can specify to transfer to odd rows (A/C/E...) or even rows (B/D/F...).\n\nThis protocol uses a custom labware definition for the Greiner Bio-One 384-well plate. When downloading the protocol, the labware definition (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons Temperature Module\n96-Well Aluminum Block\n96-Well Plate\nGreiner Bio-One 384-well plate\n\n\n\nSlot 1: Greiner Bio-One 384-well plate\nSlot 2: Opentrons 300\u00b5L Tips\nSlot 4: Opentrons Temperature Module with 96-Well Aluminum Block & 96-Well Plate containing samples in columns 1-8\n\n\nUsing the customizations field (below), set up your protocol.\n* Destination Rows: Specify which rows the multi-channel pipette will dispense in.\n* P300-Multi Mount: Select which mount (left or right) the P300-Multi is attached to.", + "description": "This protocol automates the distribution of samples from a 96-well plate (on the Temperature Module) to a 384-well plate.\n\nGiven the mapping differences between a 96-well plate and a 384-well plate, the user can specify to transfer to odd rows (A/C/E...) or even rows (B/D/F...).\n\nThis protocol uses a custom labware definition for the Greiner Bio-One 384-well plate. When downloading the protocol, the labware definition (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons Temperature Module\n96-Well Aluminum Block\n96-Well Plate\nGreiner Bio-One 384-well plate\n\n\n\nSlot 1: Greiner Bio-One 384-well plate\nSlot 2: Opentrons 300\u00b5L Tips\nSlot 4: Opentrons Temperature Module with 96-Well Aluminum Block & 96-Well Plate containing samples in columns 1-8\n\n\nUsing the customizations field (below), set up your protocol.\n Destination Rows: Specify which rows the multi-channel pipette will dispense in.\n P300-Multi Mount: Select which mount (left or right) the P300-Multi is attached to.", "internal": "060c4f", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/063611-part-2/README.json b/protoBuilds/063611-part-2/README.json index d20710082..2f91adfa8 100644 --- a/protoBuilds/063611-part-2/README.json +++ b/protoBuilds/063611-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nOpentrons p300 tips opentrons_96_tiprack_300ul (these boxes should be full) (Deck Slots 7, 8, 9)\nOpentrons p300 tips opentrons_96_tiprack_300ul (these boxes are initially empty) (Deck Slots 4, 5, 6)\n", - "description": "This protocol uses a p300 multi-channel pipette to run a separate, preparative process to put 300 ul tips into a custom arrangement required for use of a multi-channel pipette with only four tips attached on alternating nozzles for use with a custom labware rack which contains 6 columns of 4 tubes. The starting deck arrangement requires either 2, 4 or 6 tip boxes. Half of those tip boxes must be completely full while the other half must be completely empty.\nLinks:\n* Custom Cap Filling\n* Custom Tip Rack Formatting\nThis protocol was developed as a separate preparative process to set up a custom arrangement of 300 ul tips needed to use a custom rack (with 6 columns of 4 wells each) in the attached Custom Cap Filling protocol.", + "description": "This protocol uses a p300 multi-channel pipette to run a separate, preparative process to put 300 ul tips into a custom arrangement required for use of a multi-channel pipette with only four tips attached on alternating nozzles for use with a custom labware rack which contains 6 columns of 4 tubes. The starting deck arrangement requires either 2, 4 or 6 tip boxes. Half of those tip boxes must be completely full while the other half must be completely empty.\nLinks:\n Custom Cap Filling\n Custom Tip Rack Formatting\nThis protocol was developed as a separate preparative process to set up a custom arrangement of 300 ul tips needed to use a custom rack (with 6 columns of 4 wells each) in the attached Custom Cap Filling protocol.", "internal": "063611-part-2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/063611/README.json b/protoBuilds/063611/README.json index 199b9ec7d..38dc1fa87 100644 --- a/protoBuilds/063611/README.json +++ b/protoBuilds/063611/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nOpentrons p300 tips in a custom arrangement (Deck Slots 10, 11)\nCustom Racks (4 columns of 6) (Deck Slots 4,1,5,2)\nReservoir nest_1_reservoir_195ml (Deck Slot 3)\n", - "description": "This protocol uses a p300 multi-channel pipette to top-dispense 250 ul of liquid from a reservoir into as many as 96 caps housed in up to four custom racks (each rack has 6 columns of 4 caps each). The 300 ul tips are required to be in a custom arrangement (tiprack rows B, D, F, H are empty to permit a mode of non-standard, multi-channel pipetting with 4 tips mounted on alternating nozzles) to support use of custom racks having 6 columns of 4 wells each. The custom tip arrangement can be set up manually, with a separate preparative OT-2 protocol (part-2) attached on this page (recommended), or as a first step at the start of the main protocol. \nLinks:\n* Custom Cap Filling\n* Custom Tip Arranging\nThis protocol was developed to transfer 250 ul of liquid from a reservoir into as many as 96 caps arranged in columns of 4 in up to 4 custom racks. Tip change after every rack is optional. Tip tracking to keep track of the starting tip from run to run is optional. Preparation of the custom tip arrangement at the start of this main protocol is optional (recommendation is to handle tip arrangement as a separate process by using protocol Custom Tip Arranging attached above as part 2).", + "description": "This protocol uses a p300 multi-channel pipette to top-dispense 250 ul of liquid from a reservoir into as many as 96 caps housed in up to four custom racks (each rack has 6 columns of 4 caps each). The 300 ul tips are required to be in a custom arrangement (tiprack rows B, D, F, H are empty to permit a mode of non-standard, multi-channel pipetting with 4 tips mounted on alternating nozzles) to support use of custom racks having 6 columns of 4 wells each. The custom tip arrangement can be set up manually, with a separate preparative OT-2 protocol (part-2) attached on this page (recommended), or as a first step at the start of the main protocol. \nLinks:\n Custom Cap Filling\n Custom Tip Arranging\nThis protocol was developed to transfer 250 ul of liquid from a reservoir into as many as 96 caps arranged in columns of 4 in up to 4 custom racks. Tip change after every rack is optional. Tip tracking to keep track of the starting tip from run to run is optional. Preparation of the custom tip arrangement at the start of this main protocol is optional (recommendation is to handle tip arrangement as a separate process by using protocol Custom Tip Arranging attached above as part 2).", "internal": "063611", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/06da40/README.json b/protoBuilds/06da40/README.json index 3b39e9d4e..49564915b 100644 --- a/protoBuilds/06da40/README.json +++ b/protoBuilds/06da40/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol prepares plates for ddPCR with a normalization step beforehand.\nBased on a user-supplied CSV, the protocol begins by performing a normalization from the plate in deck slot 4 to the plate in deck slot 5 (allowing one to preserve their original samples).\nAfter the normalization step, there is an optional reaction mix creation step. Once reaction mix is ready, each well of the destination plate(s) receive 18\u00b5L of reaction mix.\nThe protocol finishes by adding 4\u00b5L of each sample to a well containing reaction mix, per replicate. For example, if 3 replicates are selected, 4\u00b5L of the normalized sample in A1 would be dispensed in A1, B1, and C1 of the destination plate, followed by 4\u00b5L of normalized sample from A2 to D1, E1, F1, etc.\nExplanation of complex parameters below:\n* .CSV Input File: Upload CSV file. Should include a header row and the first three rows: Well (A1), Sample Volume (\u00b5L), Dilutent Volume (\u00b5L)\n* Automate Reaction Mix Creation: Select whether to automate the creation of Reaction Mix.\n* Number of Replicates: Specify the number of replicates", + "description": "This protocol prepares plates for ddPCR with a normalization step beforehand.\nBased on a user-supplied CSV, the protocol begins by performing a normalization from the plate in deck slot 4 to the plate in deck slot 5 (allowing one to preserve their original samples).\nAfter the normalization step, there is an optional reaction mix creation step. Once reaction mix is ready, each well of the destination plate(s) receive 18\u00b5L of reaction mix.\nThe protocol finishes by adding 4\u00b5L of each sample to a well containing reaction mix, per replicate. For example, if 3 replicates are selected, 4\u00b5L of the normalized sample in A1 would be dispensed in A1, B1, and C1 of the destination plate, followed by 4\u00b5L of normalized sample from A2 to D1, E1, F1, etc.\nExplanation of complex parameters below:\n .CSV Input File: Upload CSV file. Should include a header row and the first three rows: Well (A1), Sample Volume (\u00b5L), Dilutent Volume (\u00b5L)\n Automate Reaction Mix Creation: Select whether to automate the creation of Reaction Mix.\n* Number of Replicates: Specify the number of replicates", "internal": "06da40", "labware": "\nNEST 96-Well PCR Plate 100\u00b5L\nOpentrons 24 Tube Rack with Eppendorf 1.5mL Safe-Lock Snapcap\nOpentrons Tip Rack, 20\u00b5L\nOpentrons Tip Rack, 300\u00b5L\nSemi-skirted Plate on Aluminum Block\n", "markdown": { diff --git a/protoBuilds/08878b/README.json b/protoBuilds/08878b/README.json index beeaaecfe..7c723e3dc 100644 --- a/protoBuilds/08878b/README.json +++ b/protoBuilds/08878b/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol utilizes the P300 (GEN2) and P1000 pipettes to transfer and mix reagents between their original container and destination plate.\nThe protocol begins by making four (4) dilutions of reagent with heparin or sample. These dilutions are then added to a PCR plate on the temperature module and other reagents are added.\nNote about Temperature Module: The temperature of the Temperature Module can now be set in the Opentrons App. To expedite a heating or cooling step in your protocol, you should set your Temperature Module to the desired temperature in the Opentrons App, prior to running your protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single GEN2 Pipette\nP1000 Single Pipette\nOpentrons 300\u00b5L Tiprack\nOpentrons 1000\u00b5L Tiprack\nOpentrons Temperature Module with Aluminum Block Set\nBio-Rad 96-Well Plate 200\u00b5L PCR\nOpentrons 4-in-1 Tube Rack Set (2mL and 15mL+50mL tops)\nTubes (2mL, 15mL, and 50mL) for Tube Rack\n\n\n\nFor this protocol, be sure that the pipettes (P300 Single GEN2 and P1000 Single) are attached.\nUsing the customization fields below, set up your protocol.\n* P300 Single GEN2 Mount: Specify which mount the P300 is on (left or right).\n* P1000 Single Mount: Specify which mount the P1000 is on (left or right.\n* Incubation Time (in minutes): Specify how many minutes to have have the robot wait (incubate) after adding each reagent to the samples on the temperature module.\nSlot 4: Opentrons Temperature Module with 96-Well Aluminum Block (from set) and Bio-Rad Plate, clean and empty\nSlot 5: 15mL+50mL Tube Rack\n * A1: Reagent 1 (15mL Tube)\n * A2: Reagent 2 (15mL Tube)\n * A3: Reagent 4 (50mL Tube)\n * B1: Reagent 3 (15mL Tube)\n * B2: 20% Acetic Acid (15mL Tube)\nSlot 6: 2mL Tube Rack with 2mL tubes in A1-A5 and B1-B5\n * A1: Heparin Standard\n * B1: Sample\n * Remaining tubes should be empty to begin\nSlot 5: 12 Column Reservoir\n * Column 1: Proeinase K\n * Column 3: Lysis Solution\n * Column 5: Magnetic Beads\n * Column 7: Elution\nSlot 8: Opentrons 300\u00b5L Tiprack\nSlot 9: Opentrons 1000\u00b5L Tiprack\nSlot 11: Opentrons 300\u00b5L Tiprack", + "description": "This protocol utilizes the P300 (GEN2) and P1000 pipettes to transfer and mix reagents between their original container and destination plate.\nThe protocol begins by making four (4) dilutions of reagent with heparin or sample. These dilutions are then added to a PCR plate on the temperature module and other reagents are added.\nNote about Temperature Module: The temperature of the Temperature Module can now be set in the Opentrons App. To expedite a heating or cooling step in your protocol, you should set your Temperature Module to the desired temperature in the Opentrons App, prior to running your protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single GEN2 Pipette\nP1000 Single Pipette\nOpentrons 300\u00b5L Tiprack\nOpentrons 1000\u00b5L Tiprack\nOpentrons Temperature Module with Aluminum Block Set\nBio-Rad 96-Well Plate 200\u00b5L PCR\nOpentrons 4-in-1 Tube Rack Set (2mL and 15mL+50mL tops)\nTubes (2mL, 15mL, and 50mL) for Tube Rack\n\n\n\nFor this protocol, be sure that the pipettes (P300 Single GEN2 and P1000 Single) are attached.\nUsing the customization fields below, set up your protocol.\n P300 Single GEN2 Mount: Specify which mount the P300 is on (left or right).\n P1000 Single Mount: Specify which mount the P1000 is on (left or right.\n* Incubation Time (in minutes): Specify how many minutes to have have the robot wait (incubate) after adding each reagent to the samples on the temperature module.\nSlot 4: Opentrons Temperature Module with 96-Well Aluminum Block (from set) and Bio-Rad Plate, clean and empty\nSlot 5: 15mL+50mL Tube Rack\n * A1: Reagent 1 (15mL Tube)\n * A2: Reagent 2 (15mL Tube)\n * A3: Reagent 4 (50mL Tube)\n * B1: Reagent 3 (15mL Tube)\n * B2: 20% Acetic Acid (15mL Tube)\nSlot 6: 2mL Tube Rack with 2mL tubes in A1-A5 and B1-B5\n * A1: Heparin Standard\n * B1: Sample\n * Remaining tubes should be empty to begin\nSlot 5: 12 Column Reservoir\n * Column 1: Proeinase K\n * Column 3: Lysis Solution\n * Column 5: Magnetic Beads\n * Column 7: Elution\nSlot 8: Opentrons 300\u00b5L Tiprack\nSlot 9: Opentrons 1000\u00b5L Tiprack\nSlot 11: Opentrons 300\u00b5L Tiprack", "internal": "08878b", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/089108/README.json b/protoBuilds/089108/README.json index f49bfdca4..4b56e3465 100644 --- a/protoBuilds/089108/README.json +++ b/protoBuilds/089108/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol performs the 96-well Plasmid ezFilter Miniprep Kit. For a detailed list of protocol steps, please see below.\nExplanation of complex parameters below:\n* Number of plates: Specify whether using 1 (slot 2 alone) or two (slots 2 and 5) plates for this run.\n* Number of Samples Plate 1 & 2: Select the number of samples per plate. If the number of plates variable = 1 above, then the number of samples for plate 2 will be ignored.\n* P300 Mount: Specify which mount (left or right) to host the P300 Multi-Channel Pipette\n", + "description": "This protocol performs the 96-well Plasmid ezFilter Miniprep Kit. For a detailed list of protocol steps, please see below.\nExplanation of complex parameters below:\n Number of plates: Specify whether using 1 (slot 2 alone) or two (slots 2 and 5) plates for this run.\n Number of Samples Plate 1 & 2: Select the number of samples per plate. If the number of plates variable = 1 above, then the number of samples for plate 2 will be ignored.\n* P300 Mount: Specify which mount (left or right) to host the P300 Multi-Channel Pipette\n", "internal": "089108", "labware": "\nNEST 1 Well Reservoir\nOpentrons 300ul Tips\nNEST 1 Well Reservoir\nUSA Scientific 96 Deepwell Plate 2.4mL\nCustom 96 plates\n", "markdown": { diff --git a/protoBuilds/08e3eb/README.json b/protoBuilds/08e3eb/README.json index b1861e0e8..675d9901e 100644 --- a/protoBuilds/08e3eb/README.json +++ b/protoBuilds/08e3eb/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol automates the distribution of assays from a 48-well reservoir to 9, 96-well plates.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many \"runs\" to perform. During each run, all 9 plates will be filled with assay from the reservoir. At the conclusion of filling the 9 plates, the OT-2 will flash, pause, and prompt the user to replace the plates on the deck.\n\nThis protocol uses custom labware definitions for the 48-well reservoir (Agilent) and 96-well plate (MicroAmp Endura). When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nAgilent 48-Well Reservoir\nMicroAmp Endura 96-Well Plate\nReagents\n\n\n\nSlot 1: MicroAmp Endura 96-Well Plate\nSlot 2: MicroAmp Endura 96-Well Plate\nSlot 3: MicroAmp Endura 96-Well Plate\nSlot 4: MicroAmp Endura 96-Well Plate\nSlot 5: MicroAmp Endura 96-Well Plate\nSlot 6: MicroAmp Endura 96-Well Plate\nSlot 7: MicroAmp Endura 96-Well Plate\nSlot 8: MicroAmp Endura 96-Well Plate\nSlot 9: MicroAmp Endura 96-Well Plate\nSlot 10: Opentrons 50/300\u00b5L Tips\nSlot 11: Agilent 48-Well Reservoir with Reagents\n\n\nUsing the customizations field (below), set up your protocol.\n* Starting Tip Column: Specify which column of tips to begin drawing from. Over the course of the protocol, the multi-channel pipette will pick up tips from\n* P300-Multi Mount: Select which mount (left or right) the P300-Multi is attached to.", + "description": "This protocol automates the distribution of assays from a 48-well reservoir to 9, 96-well plates.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many \"runs\" to perform. During each run, all 9 plates will be filled with assay from the reservoir. At the conclusion of filling the 9 plates, the OT-2 will flash, pause, and prompt the user to replace the plates on the deck.\n\nThis protocol uses custom labware definitions for the 48-well reservoir (Agilent) and 96-well plate (MicroAmp Endura). When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nAgilent 48-Well Reservoir\nMicroAmp Endura 96-Well Plate\nReagents\n\n\n\nSlot 1: MicroAmp Endura 96-Well Plate\nSlot 2: MicroAmp Endura 96-Well Plate\nSlot 3: MicroAmp Endura 96-Well Plate\nSlot 4: MicroAmp Endura 96-Well Plate\nSlot 5: MicroAmp Endura 96-Well Plate\nSlot 6: MicroAmp Endura 96-Well Plate\nSlot 7: MicroAmp Endura 96-Well Plate\nSlot 8: MicroAmp Endura 96-Well Plate\nSlot 9: MicroAmp Endura 96-Well Plate\nSlot 10: Opentrons 50/300\u00b5L Tips\nSlot 11: Agilent 48-Well Reservoir with Reagents\n\n\nUsing the customizations field (below), set up your protocol.\n Starting Tip Column: Specify which column of tips to begin drawing from. Over the course of the protocol, the multi-channel pipette will pick up tips from\n P300-Multi Mount: Select which mount (left or right) the P300-Multi is attached to.", "internal": "08e3eb", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/0944e4/README.json b/protoBuilds/0944e4/README.json index 66bf1e694..977b48de1 100644 --- a/protoBuilds/0944e4/README.json +++ b/protoBuilds/0944e4/README.json @@ -5,7 +5,7 @@ "Ampure XP" ] }, - "description": "This protocol performs a custom NGS library cleanup using Ampure XP beads in a variable ratio with samples. The samples are mounted on an Opentrons magnetic module, and the final elute is transferred to a fresh PCR plate.\n\n\n\nOpentrons Magnetic Module GEN2\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nEppendorf twin.tec 96-well PCR plate #0030129512\nP20 multi-channel GEN2 electronic pipette\nP300 multi-channel electronic pipette\nOpentrons 20ul filter tiprack\nOpentrons 200ul filter tiprack\n\n\n\n12-channel reservoir (slot 7)\n* channel 1: Ampure XP beads\n* channel 2: 80% ethanol\n* channel 3: EB buffer\n* channels 11-12: liquid waste (loaded empty)", + "description": "This protocol performs a custom NGS library cleanup using Ampure XP beads in a variable ratio with samples. The samples are mounted on an Opentrons magnetic module, and the final elute is transferred to a fresh PCR plate.\n\n\n\nOpentrons Magnetic Module GEN2\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nEppendorf twin.tec 96-well PCR plate #0030129512\nP20 multi-channel GEN2 electronic pipette\nP300 multi-channel electronic pipette\nOpentrons 20ul filter tiprack\nOpentrons 200ul filter tiprack\n\n\n\n12-channel reservoir (slot 7)\n channel 1: Ampure XP beads\n channel 2: 80% ethanol\n channel 3: EB buffer\n channels 11-12: liquid waste (loaded empty)", "internal": "0944e4", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/0a33e8/README.json b/protoBuilds/0a33e8/README.json index b625aea78..bce09ae2a 100644 --- a/protoBuilds/0a33e8/README.json +++ b/protoBuilds/0a33e8/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps a 384 well plate with 5ul from (4) 96 deep well plates as the source. Deepwell plates should be placed in order of slot 4, 1, 5, 2 as sample number increases, with tips placed in order of slot 10, 7, 11, and 8. Samples in Plate 1 on slot 4 are completely transferred before moving onto Plate 2 on slot 1, so on and so forth. Plate 1 (slot 4) is dispensed into A1-A23 of the 384 plate, Plate 2 (slot 1) -> B1-B23 of the 384 plate, Plate 3 (slot 5) -> A2-A24 of the 384 plate, Plate 4 (slot 2) -> B2-B24 of the 384 plate. Negative and positive controls should be pre-loaded into O24 and P24 of the 384 well plate, and thus G12 and H12 of the Plate 4 on slot 2 should be empty.\nExplanation of complex parameters below:\n* Number of Samples (1-382): Specify number of samples for this run. Negative and positive controls are always in O24 and P24 of the 384 plate, and so samples should not be placed in G12 and H12 of plate 4 on slot 2.\n* P20 Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n", + "description": "This protocol preps a 384 well plate with 5ul from (4) 96 deep well plates as the source. Deepwell plates should be placed in order of slot 4, 1, 5, 2 as sample number increases, with tips placed in order of slot 10, 7, 11, and 8. Samples in Plate 1 on slot 4 are completely transferred before moving onto Plate 2 on slot 1, so on and so forth. Plate 1 (slot 4) is dispensed into A1-A23 of the 384 plate, Plate 2 (slot 1) -> B1-B23 of the 384 plate, Plate 3 (slot 5) -> A2-A24 of the 384 plate, Plate 4 (slot 2) -> B2-B24 of the 384 plate. Negative and positive controls should be pre-loaded into O24 and P24 of the 384 well plate, and thus G12 and H12 of the Plate 4 on slot 2 should be empty.\nExplanation of complex parameters below:\n Number of Samples (1-382): Specify number of samples for this run. Negative and positive controls are always in O24 and P24 of the 384 plate, and so samples should not be placed in G12 and H12 of plate 4 on slot 2.\n P20 Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n", "internal": "0a33e8", "labware": "\nThermofisher 96 well plate\nThermofisher 384 well plate\n", "markdown": { diff --git a/protoBuilds/0add76/README.json b/protoBuilds/0add76/README.json index f1cec74ca..c3d07a123 100644 --- a/protoBuilds/0add76/README.json +++ b/protoBuilds/0add76/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol utilizes a CSV (.csv) file to dictate transfers of two reagents (DNA Stock and Water) to a VWR 96-well PCR plate. Simply upload the properly formatted CSV (examples below), set parameters, then download your protocol for use with the OT-2.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\n[P10 Single Pipette]\nP300 Single Pipette\nGEB 96 Tip Rack 10 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\nVWR Universal Pipet Tips 10ul, XL, Low Retention\nVWR Universal Pipet Tips 300ul, Low Retention\nVWR Flat 96 Well PCR Plate 200ul\nVWR Microplate 96 Square 2ml\nEK Scientific Reservoir Without Lid 290 mL\n\n\n\nFor this protocol, be sure that the pipettes (P10 and P50) are attached.\nUsing the customization fields below, set up your protocol.\n* Transfer CSV: Upload your properly formatted (see below) CSV.\n* P10 Single Mount: Specify which mount the P10 is on (left or right).\n* P300 Single Mount: Specify which mount the P50 is on (left or right).\nNote about CSV\nThe CSV should be formatted like so:\nSamples | DNA Stock Volume (\u00b5L) | H20 Stock Volume (\u00b5L) | Well\nThe first row (A1, B1, C1, D1) can contain headers (like above) or simply have the desired information. All of the following rows should just have the necessary information.\nLabware Setup\nSlot 6: EK Scientific Reservoir Without Lid 290 mL\nSlot 8: VWR Flat 96 Well PCR Plate 200ul\nSlot 9: Opentrons 96 Tip Rack 300 \u00b5L\nSlot 10: VWR Square Microplate 96 Square 2ml\nSlot 11: GEB 96 Tip Rack 10 \u00b5L", + "description": "This protocol utilizes a CSV (.csv) file to dictate transfers of two reagents (DNA Stock and Water) to a VWR 96-well PCR plate. Simply upload the properly formatted CSV (examples below), set parameters, then download your protocol for use with the OT-2.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\n[P10 Single Pipette]\nP300 Single Pipette\nGEB 96 Tip Rack 10 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\nVWR Universal Pipet Tips 10ul, XL, Low Retention\nVWR Universal Pipet Tips 300ul, Low Retention\nVWR Flat 96 Well PCR Plate 200ul\nVWR Microplate 96 Square 2ml\nEK Scientific Reservoir Without Lid 290 mL\n\n\n\nFor this protocol, be sure that the pipettes (P10 and P50) are attached.\nUsing the customization fields below, set up your protocol.\n Transfer CSV: Upload your properly formatted (see below) CSV.\n P10 Single Mount: Specify which mount the P10 is on (left or right).\n* P300 Single Mount: Specify which mount the P50 is on (left or right).\nNote about CSV\nThe CSV should be formatted like so:\nSamples | DNA Stock Volume (\u00b5L) | H20 Stock Volume (\u00b5L) | Well\nThe first row (A1, B1, C1, D1) can contain headers (like above) or simply have the desired information. All of the following rows should just have the necessary information.\nLabware Setup\nSlot 6: EK Scientific Reservoir Without Lid 290 mL\nSlot 8: VWR Flat 96 Well PCR Plate 200ul\nSlot 9: Opentrons 96 Tip Rack 300 \u00b5L\nSlot 10: VWR Square Microplate 96 Square 2ml\nSlot 11: GEB 96 Tip Rack 10 \u00b5L", "internal": "0add76", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/0aee8a/README.json b/protoBuilds/0aee8a/README.json index 1bb25f64c..cae88612f 100644 --- a/protoBuilds/0aee8a/README.json +++ b/protoBuilds/0aee8a/README.json @@ -5,7 +5,7 @@ "Serial Dilution" ] }, - "deck-setup": "Volume Definitions:\n* VOL1= DMSO transfer volume for vertical plates (post dilution volume) \n* VOL2= DMSO transfer volume for horizontal plates (post dilution volume)\n* VOL3= Compound C predilution volume DMSO (optional)\n* VOL4= Compound D predilution volume DMSO (optional)\n* VOL5= Compound A predilution volume DMSO (optional)\n* VOL6= Compound B predilution volume DMSO (optional)\n* VOL7= Compound C predilution volume compound (optional)\n* VOL8= Compound D predilution volume compound (optional)\n* VOL9= Compound A predilution volume compound (optional)\n* VOL10= Compound B predilution volume compound (optional)\n* VOL11= Compound C/D initial volume \n* VOL12= Compound C/D Serial dilution volume \n* VOL13= Compound A/B initial volume\n* VOL14= Compound A/B serial dilution volume\n* VOL15= Final plate volume for integra transfer ", + "deck-setup": "Volume Definitions:\n VOL1= DMSO transfer volume for vertical plates (post dilution volume) \n VOL2= DMSO transfer volume for horizontal plates (post dilution volume)\n VOL3= Compound C predilution volume DMSO (optional)\n VOL4= Compound D predilution volume DMSO (optional)\n VOL5= Compound A predilution volume DMSO (optional)\n VOL6= Compound B predilution volume DMSO (optional)\n VOL7= Compound C predilution volume compound (optional)\n VOL8= Compound D predilution volume compound (optional)\n VOL9= Compound A predilution volume compound (optional)\n VOL10= Compound B predilution volume compound (optional)\n VOL11= Compound C/D initial volume \n VOL12= Compound C/D Serial dilution volume \n VOL13= Compound A/B initial volume\n VOL14= Compound A/B serial dilution volume\n* VOL15= Final plate volume for integra transfer ", "description": "This protocol outlines serial dilution of compound stock. There is an optional predilution step for each compounds involved. For detailed protocol steps, please see below. Labware setup consists of NEST 12 well 15mL reservoir in slot 1, Nest 96 well 100 uL plate in slot 2,4,5,7,8,10 & 11 as well as P20 filter tips in slot 3 and P200 filter tips in slot 6.", "internal": "0aee8a", "labware": "\nOpentrons 200ul Filter Tips \nOpentrons 20ul Filter Tips\nNEST 12-Well Reservoirs 15mL\n", diff --git a/protoBuilds/0b97ae-protocol-2A/README.json b/protoBuilds/0b97ae-protocol-2A/README.json index 669a4dfaa..21d084eda 100644 --- a/protoBuilds/0b97ae-protocol-2A/README.json +++ b/protoBuilds/0b97ae-protocol-2A/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This is Part 2 to the QIAseq FastSelect Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nLinks:\n* Part 1: Sample Normalization\n* Part 2: QIAseq FastSelect Fragmentation", + "description": "This is Part 2 to the QIAseq FastSelect Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nLinks:\n Part 1: Sample Normalization\n Part 2: QIAseq FastSelect Fragmentation", "internal": "0b97ae-protocol-2A", "labware": "\nPerkin Elmer 12 Reservoir 21000 \u00b5L\nApplied Biosystems Enduraplate 96 Aluminum Block 220 \u00b5L\nOpentrons 96 Tip Rack 20 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0b97ae-protocol-2B/README.json b/protoBuilds/0b97ae-protocol-2B/README.json index ae43af3ce..6cba7ecb3 100644 --- a/protoBuilds/0b97ae-protocol-2B/README.json +++ b/protoBuilds/0b97ae-protocol-2B/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This is Part 2 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 3 to this protocol is the Extraction and Clean-Up steps.\nLinks:\n* Part 1: Sample Normalization\n* Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation\n* Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction", + "description": "This is Part 2 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 3 to this protocol is the Extraction and Clean-Up steps.\nLinks:\n Part 1: Sample Normalization\n Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation\n* Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction", "internal": "0b97ae-protocol-2B", "labware": "\nPerkin Elmer 12 Reservoir 21000 \u00b5L\nApplied Biosystems Enduraplate 96 Aluminum Block 220 \u00b5L\nOpentrons 96 Tip Rack 20 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0b97ae-protocol-3B/README.json b/protoBuilds/0b97ae-protocol-3B/README.json index 62dd7277f..ea26a58e6 100644 --- a/protoBuilds/0b97ae-protocol-3B/README.json +++ b/protoBuilds/0b97ae-protocol-3B/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nWater Reservoir (slot 2):\n Column 1: Nuclease Free Water\n Column 2: Binding Buffer\n Column 3 & 4: Ethanol\n Column 10, 11 & 12: Empty for Supernatent Removal\nDiluted RNA Plate (slot 7 Temperature Module):\n RNA Samples Starting Plate\nReagent Plate (Slot 10):\n Column 1: MasterMix\n Column 2: Magentic Beads", - "description": "This is Part 3 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 2 to this protocol is the Fragementation.\nLinks:\n* Part 1: Sample Normalization\n* Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation\n* Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction", + "description": "This is Part 3 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 2 to this protocol is the Fragementation.\nLinks:\n Part 1: Sample Normalization\n Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation\n* Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction", "internal": "0b97ae-protocol-3B", "labware": "\nPerkin Elmer 12 Reservoir 21000 \u00b5L\nApplied Biosystems Enduraplate 96 Aluminum Block 220 \u00b5L\nBio-Rad 96 Well Plate 200 \u00b5L PCR #hsp9601\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nNEST 96 Deepwell Plate 2mL #503001\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0b97ae/README.json b/protoBuilds/0b97ae/README.json index e2d56344b..118af11dd 100644 --- a/protoBuilds/0b97ae/README.json +++ b/protoBuilds/0b97ae/README.json @@ -31,6 +31,6 @@ "pipettes": "\nOpentrons P300 Single Channel Electronic Pipette (GEN2)\nOpentrons P20 Single Channel Electronic Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit \"Run\".\n", "protocol-steps": "\nLoad CSV into the slot above, With the Columns being RNA Concentration, Goal Concentration and Total Goal Volume\nThe Source Plate will be loaded onto the Temperature module on slot 10\nThe Dilution Plate will be loaded onto the Temperature module on slot 7\n", - "reagent-setup": "", + "reagent-setup": ".jpg)", "title": "QIAseq FastSelect Normalization" } \ No newline at end of file diff --git a/protoBuilds/0b98cc/README.json b/protoBuilds/0b98cc/README.json index 04ae77784..afbdfa31a 100644 --- a/protoBuilds/0b98cc/README.json +++ b/protoBuilds/0b98cc/README.json @@ -5,7 +5,7 @@ "Serial Dilution" ] }, - "description": "This protocol performs viral titration (serial dilution) of viral samples. It adds media to the dilution plates and then begins the serial dilution process of up to 12 columns worth of samples. It will dilute the samples in one of four dilution plates and then add it to the analysis dish in a specific order (skipping 3 columns for every dilution).\n\n\n\nOpentrons 200uL Filter Tips\nCorning 96 Well Round Bottom 1mL\nCorning 96-well Flat Clear Bottom Black Polystyrene TC-treated Microplate\nNEST 1 Well 195mL Reservoir\nP300 Multichannel GEN2\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nNote: The Dilution Plates utilize the Corning 96 Well Round Bottom 1mL and the Analysis Dishes utilize the Corning 96-well Flat Clear Bottom Black Polystyrene TC-treated Microplate.\n\nLabware Type\n* Dilution Plate: Corning 96 Well Round Bottom 1mL\n* Analysis Dish: Corning 96-well Flat Clear Bottom Black Polystyrene TC-treated Microplate\n* Samples: NEST 96 Well Plate 100uL PCR Full Skirt\n* Media Reservoir: NEST 1 Well 195mL Reservoir\nProtocol Steps\n1. Transfer appropriate volumes of media from the reservoir to each dilution plate on a per column basis using the multichannel pipette.\n2. Sample from the first column (A1) is transferred to A1 of Dilution Plate 1 where it is mixed and then transffered to A1 on analysis dish 1.\n3. Diluted sample is transferred from A1 of Dilution Plate 1 to A1 of Dilution Plate 2. It is thoroughly mixed and then transferred to A4 on Analysis Dish 1.\n4. Diluted sample is transferred from A1 of Dilution Plate 2 to A1 of Dilution Plate 3. It is thoroughly mixed and then transferred to A7 on Analysis Dish 1.\n5. Diluted sample is transferred from A1 of Dilution Plate 3 to A1 of Dilution Plate 4. It is thoroughly mixed and then transferred to A10 on Analysis Dish 1.\n6. This completes one set of samples. This cycle will repeat for up to 12 columns worth of samples across four analysis dishes.", + "description": "This protocol performs viral titration (serial dilution) of viral samples. It adds media to the dilution plates and then begins the serial dilution process of up to 12 columns worth of samples. It will dilute the samples in one of four dilution plates and then add it to the analysis dish in a specific order (skipping 3 columns for every dilution).\n\n\n\nOpentrons 200uL Filter Tips\nCorning 96 Well Round Bottom 1mL\nCorning 96-well Flat Clear Bottom Black Polystyrene TC-treated Microplate\nNEST 1 Well 195mL Reservoir\nP300 Multichannel GEN2\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nNote: The Dilution Plates utilize the Corning 96 Well Round Bottom 1mL and the Analysis Dishes utilize the Corning 96-well Flat Clear Bottom Black Polystyrene TC-treated Microplate.\n\nLabware Type\n Dilution Plate: Corning 96 Well Round Bottom 1mL\n Analysis Dish: Corning 96-well Flat Clear Bottom Black Polystyrene TC-treated Microplate\n Samples: NEST 96 Well Plate 100uL PCR Full Skirt\n Media Reservoir: NEST 1 Well 195mL Reservoir\nProtocol Steps\n1. Transfer appropriate volumes of media from the reservoir to each dilution plate on a per column basis using the multichannel pipette.\n2. Sample from the first column (A1) is transferred to A1 of Dilution Plate 1 where it is mixed and then transffered to A1 on analysis dish 1.\n3. Diluted sample is transferred from A1 of Dilution Plate 1 to A1 of Dilution Plate 2. It is thoroughly mixed and then transferred to A4 on Analysis Dish 1.\n4. Diluted sample is transferred from A1 of Dilution Plate 2 to A1 of Dilution Plate 3. It is thoroughly mixed and then transferred to A7 on Analysis Dish 1.\n5. Diluted sample is transferred from A1 of Dilution Plate 3 to A1 of Dilution Plate 4. It is thoroughly mixed and then transferred to A10 on Analysis Dish 1.\n6. This completes one set of samples. This cycle will repeat for up to 12 columns worth of samples across four analysis dishes.", "internal": "0b98cc", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/0bf4f4-pt2/README.json b/protoBuilds/0bf4f4-pt2/README.json index 00141ef41..28abd0372 100644 --- a/protoBuilds/0bf4f4-pt2/README.json +++ b/protoBuilds/0bf4f4-pt2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck setup with a full plate of samples. Tip rack on slot 11 will be used to park tips in ethanol wash steps.\n\n", - "description": "This protocol is part 2 of a 3 part series which preps a 96 well Bio-Rad 200ul plate in accordance with the Ilumina DNA Prep Kit.\n\nPart 1: Tagment DNA\nPart 3: Cleanup libraries\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples for this run.\n* Index start column: Specify which column to start aspirating from on the index plate.\n* P300 tip start column on slot 11 (1-12): The number of columns of tips used on slot 11 is equal to the number of columns of samples. Slot 11 tip rack is used for tip parking on the two ethanol washes to save tips. Specify which column to start picking tips up from.\n* Length from side: Specify the length from the side of the well to aspirate from magnetically engaged beads. A value of 1 would be 1mm from the side of the well opposite beads. A value of 2.73 means the exact center of the well. This distance is also used when re-suspending beads, and mixing at bead location.\n* Aspiration height: Specify how many millimeters from the bottom of the well to aspirate from at the Length from side distance specified above.\n* P20 Multi-Channel GEN2 Mount: Specify which side (left or right) the P20 multi channel pipette is mounted.\n* P300 Multi Channel GEN2 Mount: Specify which side (left or right) the P300 multi channel pipette is mounted.", + "description": "This protocol is part 2 of a 3 part series which preps a 96 well Bio-Rad 200ul plate in accordance with the Ilumina DNA Prep Kit.\n\nPart 1: Tagment DNA\nPart 3: Cleanup libraries\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples for this run.\n Index start column: Specify which column to start aspirating from on the index plate.\n P300 tip start column on slot 11 (1-12): The number of columns of tips used on slot 11 is equal to the number of columns of samples. Slot 11 tip rack is used for tip parking on the two ethanol washes to save tips. Specify which column to start picking tips up from.\n Length from side: Specify the length from the side of the well to aspirate from magnetically engaged beads. A value of 1 would be 1mm from the side of the well opposite beads. A value of 2.73 means the exact center of the well. This distance is also used when re-suspending beads, and mixing at bead location.\n Aspiration height: Specify how many millimeters from the bottom of the well to aspirate from at the Length from side distance specified above.\n P20 Multi-Channel GEN2 Mount: Specify which side (left or right) the P20 multi channel pipette is mounted.\n* P300 Multi Channel GEN2 Mount: Specify which side (left or right) the P300 multi channel pipette is mounted.", "internal": "0bf4f4-pt2", "labware": "\nBio-RAD 96 well plate 200ul\nNest 12 Well Reservoir 15mL\nOpentrons 20ul Filter Tip Rack\nOpentrons 200ul Filter Tip Rack\n", "markdown": { diff --git a/protoBuilds/0bf4f4-pt3/README.json b/protoBuilds/0bf4f4-pt3/README.json index 46687ae2a..a91cfb80d 100644 --- a/protoBuilds/0bf4f4-pt3/README.json +++ b/protoBuilds/0bf4f4-pt3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck setup with a full plate of samples and pre-populated mag beads in Plate B. Note: if the protocol runs out of tips, it will pause and prompt the user to replace all tip racks. Tip boxes will be used in the order of the following slots for 200ul tips: Slot 7, 8, 9, 10. Tip rack on slot 11 will always be used for the ethanol wash step, as it will use parked tips, no matter how many samples. \n\n", - "description": "This protocol is part 3 of a 3 part series which preps a 96 well Bio-Rad 200ul plate in accordance with the Ilumina DNA Prep Kit.\n\nPart 1: Tagment DNA\nPart 2: Cleanup libraries\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples for this run.\n* Plate A Start Column: Specify which column to start on plate A.\n* Plate B Start Column: Specify which column to start on plate B.\n* Plate C Start Column: Specify which column to start on plate C.\n* P300 tip start column on slot 11 (1-12): The number of columns of tips used on slot 11 is equal to the number of columns of samples. Slot 11 tip rack is used for tip parking on the two ethanol washes to save tips. Specify which column to start picking tips up from.\n* Length from side: Specify the length from the side of the well to aspirate from magnetically engaged beads. A value of 1 would be 1mm from the side of the well opposite beads. A value of 2.73 means the exact center of the well. This distance is also used when re-suspending beads, and mixing at bead location.\n* Aspiration height: Specify how many millimeters from the bottom of the well to aspirate from at the Length from side distance specified above.\n* P20 Multi-Channel GEN2 Mount: Specify which side (left or right) the P20 multi channel pipette is mounted.\n* P300 Multi Channel GEN2 Mount: Specify which side (left or right) the P300 multi channel pipette is mounted.", + "description": "This protocol is part 3 of a 3 part series which preps a 96 well Bio-Rad 200ul plate in accordance with the Ilumina DNA Prep Kit.\n\nPart 1: Tagment DNA\nPart 2: Cleanup libraries\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples for this run.\n Plate A Start Column: Specify which column to start on plate A.\n Plate B Start Column: Specify which column to start on plate B.\n Plate C Start Column: Specify which column to start on plate C.\n P300 tip start column on slot 11 (1-12): The number of columns of tips used on slot 11 is equal to the number of columns of samples. Slot 11 tip rack is used for tip parking on the two ethanol washes to save tips. Specify which column to start picking tips up from.\n Length from side: Specify the length from the side of the well to aspirate from magnetically engaged beads. A value of 1 would be 1mm from the side of the well opposite beads. A value of 2.73 means the exact center of the well. This distance is also used when re-suspending beads, and mixing at bead location.\n Aspiration height: Specify how many millimeters from the bottom of the well to aspirate from at the Length from side distance specified above.\n P20 Multi-Channel GEN2 Mount: Specify which side (left or right) the P20 multi channel pipette is mounted.\n* P300 Multi Channel GEN2 Mount: Specify which side (left or right) the P300 multi channel pipette is mounted.", "internal": "0bf4f4-pt3", "labware": "\nBio-RAD 96 well plate 200ul\nNest 12 Well Reservoir 15mL\nOpentrons 20ul Filter Tip Rack\nOpentrons 200ul Filter Tip Rack\n", "markdown": { diff --git a/protoBuilds/0bf4f4/README.json b/protoBuilds/0bf4f4/README.json index 9ddf3b082..c03c70d32 100644 --- a/protoBuilds/0bf4f4/README.json +++ b/protoBuilds/0bf4f4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck setup with a full plate of samples. Mastermix is always kept in column 1 regardless of number of samples, as is water in the first column of the Nest 12 well reservoir.\n\n\n", - "description": "This protocol is part 1 of a 3 part series which preps a 96 well Bio-Rad 200ul plate with diluted DNA and mastermix in accordance with the Ilumina DNA Prep Kit. DNA is diluted with water before mastermix is added. Find part 2 and part 3 of protocol below:\n\nPart 2: Post Tagmentation Cleanup\nPart 3: Cleanup libraries\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples for this run.\n* P300 Tip Start Column on Slot 8 (1-12): One column of the 200ul tip rack will be used per run. Specify which column to pick up tips from for this run.\n* P20 Multi-Channel GEN2 Mount: Specify which side (left or right) the P20 multi channel pipette is mounted.\n* P300 Multi Channel GEN2 Mount: Specify which side (left or right) the P300 multi channel pipette is mounted.", + "description": "This protocol is part 1 of a 3 part series which preps a 96 well Bio-Rad 200ul plate with diluted DNA and mastermix in accordance with the Ilumina DNA Prep Kit. DNA is diluted with water before mastermix is added. Find part 2 and part 3 of protocol below:\n\nPart 2: Post Tagmentation Cleanup\nPart 3: Cleanup libraries\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples for this run.\n P300 Tip Start Column on Slot 8 (1-12): One column of the 200ul tip rack will be used per run. Specify which column to pick up tips from for this run.\n P20 Multi-Channel GEN2 Mount: Specify which side (left or right) the P20 multi channel pipette is mounted.\n P300 Multi Channel GEN2 Mount: Specify which side (left or right) the P300 multi channel pipette is mounted.", "internal": "0bf4f4", "labware": "\nBio-RAD 96 well plate 200ul\nNest 12 Well Reservoir 15mL\nOpentrons 20ul Filter Tip Rack\nOpentrons 200ul Filter Tip Rack\n", "markdown": { diff --git a/protoBuilds/0c24ca/0c24ca.ot2.apiv2.py.json b/protoBuilds/0c24ca/0c24ca.ot2.apiv2.py.json index 030694ec9..3f5ba53ea 100644 --- a/protoBuilds/0c24ca/0c24ca.ot2.apiv2.py.json +++ b/protoBuilds/0c24ca/0c24ca.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "import math\nfrom opentrons import protocol_api\n\nmetadata = {\n 'protocolName': 'Adding Transfection and Sample to Plate',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [csv_samp, number_05_plates, number_14_plates, remove_tube_vol, dest_plate,\n add_transfection_mix, trans_mix_vol,\n init_vol_50, p20_mount, p300_mount] = get_values( # noqa: F821\n \"csv_samp\", \"number_05_plates\", \"number_14_plates\", \"remove_tube_vol\",\n \"dest_plate\",\n \"add_transfection_mix\", \"trans_mix_vol\",\n \"init_vol_50\", \"p20_mount\", \"p300_mount\")\n\n # labware\n source_plate_14 = [ctx.load_labware('thermofisher_96_wellplate_1400ul',\n slot) for slot in [1, 2, 3]][:number_14_plates] # noqa: E501\n source_plate_05 = [ctx.load_labware('thermofisher_96_wellplate_500ul',\n slot) for slot in [4, 5, 6]][:number_05_plates] # noqa: E501\n\n source_plate_14 = source_plate_14\n source_plate_05 = source_plate_05\n\n tuberack = ctx.load_labware('opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical', 7) # noqa: E501\n\n dest_plate = ctx.load_labware(dest_plate, 8)\n tips200 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in [10]]\n\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in [11]]\n\n csv_lines = [[val.strip() for val in line.split(',')]\n for line in csv_samp.splitlines()\n if line.split(',')[0].strip()][1:]\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips200)\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(\"Replace empty tip racks\")\n pip.reset_tipracks()\n pip.pick_up_tip()\n\n # mapping\n # liquid height tracking\n v_naught = init_vol_50*1000\n\n radius = tuberack.rows()[0][3].diameter/2\n\n h_naught = 0.85*v_naught/(math.pi*radius**2)\n\n h = h_naught\n\n def adjust_height(vol):\n nonlocal h\n\n dh = (vol/(math.pi*radius**2))*1.33\n\n h -= dh\n\n if h < 12:\n h = 1\n\n # protocol\n ctx.comment('\\n---------------ADDING TUBES TO PLATES----------------\\n\\n')\n pip = p300 if remove_tube_vol > 20 else p20\n for line in csv_lines:\n source_well_name = line[0]\n source_slot = ctx.loaded_labwares[int(line[1])]\n source_well = source_slot.wells_by_name()[source_well_name]\n\n dest_well_name = line[2]\n dest_slot = ctx.loaded_labwares[8]\n dest_well = dest_slot.wells_by_name()[dest_well_name]\n\n pick_up(pip)\n pip.aspirate(remove_tube_vol, source_well)\n pip.dispense(remove_tube_vol, dest_well)\n pip.drop_tip()\n\n if add_transfection_mix:\n pip = p300 if trans_mix_vol > 20 else p20\n trans_mix_tube = tuberack.rows()[0][3]\n for line in csv_lines:\n\n dest_well_name = line[2]\n dest_slot = ctx.loaded_labwares[8]\n dest_well = dest_slot.wells_by_name()[dest_well_name]\n\n pick_up(pip)\n pip.aspirate(trans_mix_vol, trans_mix_tube)\n adjust_height(trans_mix_vol)\n pip.dispense(trans_mix_vol, dest_well)\n pip.drop_tip()\n", + "content": "import math\nfrom opentrons import protocol_api\n\nmetadata = {\n 'protocolName': 'Adding Transfection and Sample to Plate',\n 'author': 'Rami Farawi ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n\n [csv_samp, number_05_plates, number_14_plates, remove_tube_vol, dest_plate,\n add_transfection_mix, trans_mix_vol,\n init_vol_50, p20_mount, p300_mount] = get_values( # noqa: F821\n \"csv_samp\", \"number_05_plates\", \"number_14_plates\", \"remove_tube_vol\",\n \"dest_plate\",\n \"add_transfection_mix\", \"trans_mix_vol\",\n \"init_vol_50\", \"p20_mount\", \"p300_mount\")\n\n # labware\n source_plate_14 = [ctx.load_labware('thermofisher_96_wellplate_1400ul',\n slot) for slot in [1, 2, 3]][:number_14_plates] # noqa: E501\n source_plate_05 = [ctx.load_labware('thermofisher_96_wellplate_500ul',\n slot) for slot in [4, 5, 6]][:number_05_plates] # noqa: E501\n\n source_plate_14 = source_plate_14\n source_plate_05 = source_plate_05\n\n tuberack = ctx.load_labware('opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical', 7) # noqa: E501\n\n dest_plate = ctx.load_labware(dest_plate, 8)\n tips200 = [ctx.load_labware('opentrons_96_filtertiprack_200ul', slot)\n for slot in [10]]\n\n tips20 = [ctx.load_labware('opentrons_96_filtertiprack_20ul', slot)\n for slot in [11]]\n\n csv_lines = [[val.strip() for val in line.split(',')]\n for line in csv_samp.splitlines()\n if line.split(',')[0].strip()][1:]\n\n # pipettes\n p20 = ctx.load_instrument('p20_single_gen2', p20_mount, tip_racks=tips20)\n p300 = ctx.load_instrument('p300_single_gen2', p300_mount,\n tip_racks=tips200)\n\n def pick_up(pip):\n try:\n pip.pick_up_tip()\n except protocol_api.labware.OutOfTipsError:\n ctx.pause(\"Replace empty tip racks\")\n pip.reset_tipracks()\n pip.pick_up_tip()\n\n # mapping\n # liquid height tracking\n v_naught = init_vol_50*1000\n\n radius = tuberack.rows()[0][3].diameter/2\n\n h_naught = 0.85*v_naught/(math.pi*radius**2)\n\n h = h_naught\n\n def adjust_height(vol):\n nonlocal h\n\n dh = (vol/(math.pi*radius**2))*1.33\n\n h -= dh\n\n if h < 12:\n h = 1\n\n # protocol\n ctx.comment('\\n---------------ADDING TUBES TO PLATES----------------\\n\\n')\n pip = p300 if remove_tube_vol > 20 else p20\n for line in csv_lines:\n source_well_name = line[0]\n source_slot = ctx.loaded_labwares[int(line[1])]\n source_well = source_slot.wells_by_name()[source_well_name]\n\n dest_well_name = line[2]\n dest_slot = ctx.loaded_labwares[8]\n dest_well = dest_slot.wells_by_name()[dest_well_name]\n\n pick_up(pip)\n pip.aspirate(remove_tube_vol, source_well.bottom(z=2))\n pip.dispense(remove_tube_vol, dest_well)\n pip.drop_tip()\n\n if add_transfection_mix:\n pip = p300 if trans_mix_vol > 20 else p20\n trans_mix_tube = tuberack.rows()[0][3]\n for line in csv_lines:\n\n dest_well_name = line[2]\n dest_slot = ctx.loaded_labwares[8]\n dest_well = dest_slot.wells_by_name()[dest_well_name]\n\n pick_up(pip)\n pip.aspirate(trans_mix_vol, trans_mix_tube)\n adjust_height(trans_mix_vol)\n pip.dispense(trans_mix_vol, dest_well)\n pip.drop_tip()\n", "custom_labware_defs": [ { "brand": { @@ -3426,7 +3426,7 @@ "default": 20, "label": "Sample tube removal volume", "name": "remove_tube_vol", - "type": "int" + "type": "float" }, { "label": "Destination Plate Type", @@ -3462,13 +3462,13 @@ "default": 40, "label": "Transfection mix volume", "name": "trans_mix_vol", - "type": "int" + "type": "float" }, { "default": 40, "label": "Initial volume of transfection mix in 50mL tube (mL)", "name": "init_vol_50", - "type": "int" + "type": "float" }, { "label": "P20 Single-Channel Mount", diff --git a/protoBuilds/0cded6-amplify/README.json b/protoBuilds/0cded6-amplify/README.json index 4c0d5c735..d3cc4a2b4 100644 --- a/protoBuilds/0cded6-amplify/README.json +++ b/protoBuilds/0cded6-amplify/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs Amplify cDNA for the Illumina COVIDSeq protocol.\nLinks:\n* 1. Anneal RNA\n* 2. Synthesize First Strand cDNA\n* 3. Amplify cDNA\n* 4. Tagment PCR Amplicons\n* 5. Post Tagmentation Clean Up\n* 6. Amplify Tagmented Amplicons", + "description": "This protocol performs Amplify cDNA for the Illumina COVIDSeq protocol.\nLinks:\n 1. Anneal RNA\n 2. Synthesize First Strand cDNA\n 3. Amplify cDNA\n 4. Tagment PCR Amplicons\n 5. Post Tagmentation Clean Up\n 6. Amplify Tagmented Amplicons", "internal": "0cded6", "labware": "\nQuantgene 96 Aluminum Block 200 \u00b5L\nAgilent 96 Well Plate 200 \u00b5L #5042-8502\nAgilent With Nonskirted 96 Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0cded6-amplify2/README.json b/protoBuilds/0cded6-amplify2/README.json index 48bb56da4..b9ec3d54a 100644 --- a/protoBuilds/0cded6-amplify2/README.json +++ b/protoBuilds/0cded6-amplify2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs Amplify Tagmented Amplicons for the Illumina COVIDSeq protocol.\nLinks:\n* 1. Anneal RNA\n* 2. Synthesize First Strand cDNA\n* 3. Amplify cDNA\n* 4. Tagment PCR Amplicons\n* 5. Post Tagmentation Clean Up\n* 6. Amplify Tagmented Amplicons", + "description": "This protocol performs Amplify Tagmented Amplicons for the Illumina COVIDSeq protocol.\nLinks:\n 1. Anneal RNA\n 2. Synthesize First Strand cDNA\n 3. Amplify cDNA\n 4. Tagment PCR Amplicons\n 5. Post Tagmentation Clean Up\n 6. Amplify Tagmented Amplicons", "internal": "0cded6", "labware": "\nQuantgene 96 Aluminum Block 200 \u00b5L\nAgilent 96 Well Plate 200 \u00b5L #5042-8502\nAgilent With Nonskirted 96 Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nNEST 12 Well Reservoir 15 mL #360102\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0cded6-cleanup/README.json b/protoBuilds/0cded6-cleanup/README.json index fb981c8b1..984648c89 100644 --- a/protoBuilds/0cded6-cleanup/README.json +++ b/protoBuilds/0cded6-cleanup/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs Post Tagmentation Cleanup for the Illumina COVIDSeq protocol.\nLinks:\n* 1. Anneal RNA\n* 2. Synthesize First Strand cDNA\n* 3. Amplify cDNA\n* 4. Tagment PCR Amplicons\n* 5. Post Tagmentation Clean Up\n* 6. Amplify Tagmented Amplicons", + "description": "This protocol performs Post Tagmentation Cleanup for the Illumina COVIDSeq protocol.\nLinks:\n 1. Anneal RNA\n 2. Synthesize First Strand cDNA\n 3. Amplify cDNA\n 4. Tagment PCR Amplicons\n 5. Post Tagmentation Clean Up\n 6. Amplify Tagmented Amplicons", "internal": "0cded6", "labware": "\nQuantgene 96 Aluminum Block 200 \u00b5L\nAgilent 96 Well Plate 200 \u00b5L #5042-8502\nAgilent With Nonskirted 96 Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nNEST 12 Well Reservoir 15 mL #360102\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0cded6-synthesize/README.json b/protoBuilds/0cded6-synthesize/README.json index 4c8888139..9f61e1d1b 100644 --- a/protoBuilds/0cded6-synthesize/README.json +++ b/protoBuilds/0cded6-synthesize/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs Syntehsize First Strand cDNA for the Illumina COVIDSeq protocol.\nLinks:\n* 1. Anneal RNA\n* 2. Synthesize First Strand cDNA\n* 3. Amplify cDNA\n* 4. Tagment PCR Amplicons\n* 5. Post Tagmentation Clean Up\n* 6. Amplify Tagmented Amplicons", + "description": "This protocol performs Syntehsize First Strand cDNA for the Illumina COVIDSeq protocol.\nLinks:\n 1. Anneal RNA\n 2. Synthesize First Strand cDNA\n 3. Amplify cDNA\n 4. Tagment PCR Amplicons\n 5. Post Tagmentation Clean Up\n 6. Amplify Tagmented Amplicons", "internal": "0cded6", "labware": "\nQuantgene 96 Aluminum Block 200 \u00b5L\nAgilent 96 Well Plate 200 \u00b5L #5042-8502\nAgilent With Nonskirted 96 Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0cded6-tagment/README.json b/protoBuilds/0cded6-tagment/README.json index b2687a0dd..4a2942035 100644 --- a/protoBuilds/0cded6-tagment/README.json +++ b/protoBuilds/0cded6-tagment/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs Tagment PCR Amplicons for the Illumina COVIDSeq protocol.\nLinks:\n* 1. Anneal RNA\n* 2. Synthesize First Strand cDNA\n* 3. Amplify cDNA\n* 4. Tagment PCR Amplicons\n* 5. Post Tagmentation Clean Up\n* 6. Amplify Tagmented Amplicons", + "description": "This protocol performs Tagment PCR Amplicons for the Illumina COVIDSeq protocol.\nLinks:\n 1. Anneal RNA\n 2. Synthesize First Strand cDNA\n 3. Amplify cDNA\n 4. Tagment PCR Amplicons\n 5. Post Tagmentation Clean Up\n 6. Amplify Tagmented Amplicons", "internal": "0cded6", "labware": "\nQuantgene 96 Aluminum Block 200 \u00b5L\nAgilent 96 Well Plate 200 \u00b5L #5042-8502\nAgilent With Nonskirted 96 Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0cded6/README.json b/protoBuilds/0cded6/README.json index d2a0c6064..ad6a5337e 100644 --- a/protoBuilds/0cded6/README.json +++ b/protoBuilds/0cded6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs Anneal RNA for the Illumina COVIDSeq protocol.\nLinks:\n* 1. Anneal RNA\n* 2. Synthesize First Strand cDNA\n* 3. Amplify cDNA\n* 4. Tagment PCR Amplicons\n* 5. Post Tagmentation Clean Up\n* 6. Amplify Tagmented Amplicons", + "description": "This protocol performs Anneal RNA for the Illumina COVIDSeq protocol.\nLinks:\n 1. Anneal RNA\n 2. Synthesize First Strand cDNA\n 3. Amplify cDNA\n 4. Tagment PCR Amplicons\n 5. Post Tagmentation Clean Up\n 6. Amplify Tagmented Amplicons", "internal": "0cded6", "labware": "\nQuantgene 96 Aluminum Block 200 \u00b5L\nAgilent 96 Well Plate 200 \u00b5L #5042-8502\nAgilent With Nonskirted 96 Well Plate 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { diff --git a/protoBuilds/0d2950/README.json b/protoBuilds/0d2950/README.json index 4511a73b7..467492a63 100644 --- a/protoBuilds/0d2950/README.json +++ b/protoBuilds/0d2950/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Example deck layout with 70 samples.\n\n", - "description": "This protocol preps a sample plate with up to 95 samples (with one control). Samples in the tube rack should be placed to mirror the 96 well plate: column 1 (from the bottom up) of slots 1, 4, 7, and 10, then column two (from the bottom up of the same slots), up to column 5 of the aforementioned tube racks. Then column 1 of slots 2, 5, 8, 11 up to column 3 the tube racks in the aforementioned slots.\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples that will be processed. Up to 95 samples can be run, leaving room for a control.\n* P1000 sample tube aspiration height: Specify the height (in mm) for the P1000 pipette to aspirate when visiting sample tubes. Default is 1mm.\n* P1000 sample dispense height (in plate): Specify the height (in mm) for the P1000 pipette to dispense from when visiting the plate on slot 3. Default is 1mm.\n* P1000 single GEN2 Mount: Specify which mount (left or right) to load the P1000 single channel pipette.\n", + "description": "This protocol preps a sample plate with up to 95 samples (with one control). Samples in the tube rack should be placed to mirror the 96 well plate: column 1 (from the bottom up) of slots 1, 4, 7, and 10, then column two (from the bottom up of the same slots), up to column 5 of the aforementioned tube racks. Then column 1 of slots 2, 5, 8, 11 up to column 3 the tube racks in the aforementioned slots.\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples that will be processed. Up to 95 samples can be run, leaving room for a control.\n P1000 sample tube aspiration height: Specify the height (in mm) for the P1000 pipette to aspirate when visiting sample tubes. Default is 1mm.\n P1000 sample dispense height (in plate): Specify the height (in mm) for the P1000 pipette to dispense from when visiting the plate on slot 3. Default is 1mm.\n P1000 single GEN2 Mount: Specify which mount (left or right) to load the P1000 single channel pipette.\n", "internal": "0d2950", "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 1000uL Tips\nOpentrons 4-in-1 tube rack\n", "markdown": { diff --git a/protoBuilds/0e7175-pt2/README.json b/protoBuilds/0e7175-pt2/README.json index d2a5dbacb..60ecd6423 100644 --- a/protoBuilds/0e7175-pt2/README.json +++ b/protoBuilds/0e7175-pt2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\n", - "description": "This protocol provides sample and reagents to 2 96 well plates according to the Luminex MagPlex\u00ae Microspheres kit. Column 1 of the source isopak 1 is dispensed into rows A, C, E, G of the destination plate 1 in columns 1 and 2. Column 2 of the source isopak is dispensed into rows A, C, E, G of the destination plate 1 in columns 3 and 4, etc. Column 1 of the source isopak 2 is dispensed into rows B, D, F, H of the destination plate 1 in columns 1 and 2, etc. This is then repeated for destination plate 2. Tips are removed from rows B, D, F, H of the tipracks on slot 10 and 11 to allow for the multi-channel pipette to access the isopaks. The tiprack on slot 9 should be a full tip rack.\nExplanation of complex parameters below:\n* Sample Volume: Specify the sample volume to be replicated in microliters.\n* Use middle two columns?: Specify whether using the middle two columns in source isopaks. See below for deck map if selected. If selected, the protocol will pause after the first 96 plate is filled to prompt the user to replace the alternate tip rack on slot 11.\n* Antibody Volume: Specify the sample volume to be replicated in microliters.\n* SA-PE Volume: Specify the SA-PE volume to be replicated in microliters.\n* P300 Mount: Specify which mount (left or right) to host the P300 Multi-Channel Pipette.\n", + "description": "This protocol provides sample and reagents to 2 96 well plates according to the Luminex MagPlex\u00ae Microspheres kit. Column 1 of the source isopak 1 is dispensed into rows A, C, E, G of the destination plate 1 in columns 1 and 2. Column 2 of the source isopak is dispensed into rows A, C, E, G of the destination plate 1 in columns 3 and 4, etc. Column 1 of the source isopak 2 is dispensed into rows B, D, F, H of the destination plate 1 in columns 1 and 2, etc. This is then repeated for destination plate 2. Tips are removed from rows B, D, F, H of the tipracks on slot 10 and 11 to allow for the multi-channel pipette to access the isopaks. The tiprack on slot 9 should be a full tip rack.\nExplanation of complex parameters below:\n Sample Volume: Specify the sample volume to be replicated in microliters.\n Use middle two columns?: Specify whether using the middle two columns in source isopaks. See below for deck map if selected. If selected, the protocol will pause after the first 96 plate is filled to prompt the user to replace the alternate tip rack on slot 11.\n Antibody Volume: Specify the sample volume to be replicated in microliters.\n SA-PE Volume: Specify the SA-PE volume to be replicated in microliters.\n* P300 Mount: Specify which mount (left or right) to host the P300 Multi-Channel Pipette.\n", "internal": "0e7175-pt2", "labware": "\nNEST 12 Well Reservoir 195mL\nEppendorf Isopaks\nGreiner 96 well Chimney Bottom\nOpentrons 300ul Tips\n", "markdown": { diff --git a/protoBuilds/0e7175/README.json b/protoBuilds/0e7175/README.json index 6267682a4..c98044b9e 100644 --- a/protoBuilds/0e7175/README.json +++ b/protoBuilds/0e7175/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n", - "description": "This protocol replicates 6 or 7 isopaks from 1 or 2 source isopaks depending on the sample volume specified by the user according to the Luminex MagPlex\u00ae Microspheres kit. Tips are removed from rows B, D, F, H of the tiprack to allow for the multi-channel pipette to access the isopaks.\nExplanation of complex parameters below:\n* Number of Samples: Specify whether running 24 or 48 samples. If running 24 samples, one isopak will be replicated into 7 isopaks. If running 48 samples, isopak 1 on slot 10 will supply empty isopaks in slots 1, 2, and 3, and isopak 2 on slot 11 will supply empty isopaks in slot 4, 5, and 6. See below for diagrams.\n* Use middle two columns?: Specify whether using the middle two columns in source isopak(s). If this option is selected, the middle two columns of the source isopaks will be ignored, and the middle two tubes in the destination isopaks will also be ignored for dispensing.\n* Sample Volume: Specify the sample volume to be replicated in microliters.\n* P300 Mount: Specify which mount (left or right) to host the P300 Multi-Channel Pipette.\n", + "description": "This protocol replicates 6 or 7 isopaks from 1 or 2 source isopaks depending on the sample volume specified by the user according to the Luminex MagPlex\u00ae Microspheres kit. Tips are removed from rows B, D, F, H of the tiprack to allow for the multi-channel pipette to access the isopaks.\nExplanation of complex parameters below:\n Number of Samples: Specify whether running 24 or 48 samples. If running 24 samples, one isopak will be replicated into 7 isopaks. If running 48 samples, isopak 1 on slot 10 will supply empty isopaks in slots 1, 2, and 3, and isopak 2 on slot 11 will supply empty isopaks in slot 4, 5, and 6. See below for diagrams.\n Use middle two columns?: Specify whether using the middle two columns in source isopak(s). If this option is selected, the middle two columns of the source isopaks will be ignored, and the middle two tubes in the destination isopaks will also be ignored for dispensing.\n Sample Volume: Specify the sample volume to be replicated in microliters.\n P300 Mount: Specify which mount (left or right) to host the P300 Multi-Channel Pipette.\n", "internal": "0e7175", "labware": "\nEppendorf Isopaks\nGreiner 96 well Chimney Bottom\nOpentrons 300ul Tips\n", "markdown": { diff --git a/protoBuilds/0e8e3/README.json b/protoBuilds/0e8e3/README.json index fc08802f1..ff1867ac6 100644 --- a/protoBuilds/0e8e3/README.json +++ b/protoBuilds/0e8e3/README.json @@ -27,6 +27,6 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nOpentrons P20 and P300 GEN2 Electronic Pipettes\n\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "Reagent reservoir:\n* channel 1: DNAse buffer\n* channel 2: EDTA\n* channels 3-7: dilution buffer\n* channel 8: PCR mix\n", + "reagent-setup": "Reagent reservoir:\n channel 1: DNAse buffer\n channel 2: EDTA\n channels 3-7: dilution buffer\n channel 8: PCR mix\n", "title": "PCR Prep" } \ No newline at end of file diff --git a/protoBuilds/0eaeb5/README.json b/protoBuilds/0eaeb5/README.json index 9a60f3090..754451261 100644 --- a/protoBuilds/0eaeb5/README.json +++ b/protoBuilds/0eaeb5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSlot 1: Magnetic Module + Bio-Rad 96 Well Plate 200 uL PCR (mag_plate)\nSlot 2: Bio-Rad 96 Well Plate 200 uL PCR (sample_plate) for calibration purposes. This labwared will be transferred among Slot 2, Slot 1, and external thermocycler after.\nSlot 3: Temperature Module + Bio-Rad 96 Well Plate 200 uL PCR (reagent_plate)\nSlots 4/7/6: Opentrons 96 Filter Tip Rack 200 uL\nSlots 9/8/5: Opentrons 96 Filter Tip Rack 20 uL\nSlot 10: NEST 12-Well Reservoir, 15 mL (reagent_reservoir)\nSlot 11: NEST 12-Well Reservoir, 15 mL (waste_reservoir)\n\n", - "description": "This protocol performs the CleanPlex\u00ae NGS Panel for up to 96 samples.\nThe protocol is broken down into 6 main parts:\n* 1A: Multiplex PCR (mPCR) reaction\n* 1B: Post-mPCR Purification\n* 2A: Digestion Reaction\n* 2B: Post-Digestion Purification\n* 3A: Second PCR Reaction\n* 3B: Post-Second PCR Purification\nExplanation of complex parameters below:\n* Test parameters\n * DRYRUN: The default setting is False . If set to True, the protocol will be in dry run testing mode. The pipette will return the tip to the tiprack after each liquid transfer.\n * TEST_MODE_BEADS: The default setting is False . If set to True, the protocol will be in beads testing mode. The beads incubation and magnet engaging time will be in unit of seconds rather than minutes. Meanwhile, the pipette will return the tip to the tiprack after each liquid transfer.\n* Timer parameters\n * timer_h: Set up the time for hours\n * timer_m: Set up the time for minutes\n* Flow rate parameters\n * water_rate: Set up the flow rate of transferring water liquids, unit: folds of the default speed, 1.2 means 120 % of the default speed while 0.6 indicates 60% of the default speed\n * buffer_mmx_primer_rate: Set up the flow rate of transferring buffer/mastermix/primer liquids, unit: the same as above\n * sample_rate: Set up the flow rate of transferring sample-related liquids, unit: folds of the default speed\n * beads_rate: Set up the flow rate of transferring bead liquids, unit: the same as above\n * ethanol: Set up the flow rate of transferring ethanol liquids, unit: the same as above\n* beads mixing parameters\n * beads_mix_reps: The frequencies that robot will mix the beads\n * beads_mix_rate: The flow rate that the robot will mix the beads, the same as Flow rate parameters\n* Magnetic Module parameters\n * magdeck_engage_height: The height of magnet that will engage, in mm\n * ethnaol_dis_zoffset: The height of dispensing ethanol from the top of the well during ethanol washing, in mm\n * incubation_time: The time it takes for DNA binding before engaging the magnet, unit in minutes when TEST_MODE_BEADS is False\n * beads_engaging_time: The time it takes for beads binding after engaging the magnet, unit in minutes when TEST_MODE_BEADS is False\n * airdry_time: The time it takes for airdrying after removing the enthanol, unit in minutes when TEST_MODE_BEADS is False\n * ethanol_wash_time: The time it takes for ethanol washing after adding it in the well, unit in minutes when TEST_MODE_BEADS is False\n", + "description": "This protocol performs the CleanPlex\u00ae NGS Panel for up to 96 samples.\nThe protocol is broken down into 6 main parts:\n 1A: Multiplex PCR (mPCR) reaction\n 1B: Post-mPCR Purification\n 2A: Digestion Reaction\n 2B: Post-Digestion Purification\n 3A: Second PCR Reaction\n 3B: Post-Second PCR Purification\nExplanation of complex parameters below:\n Test parameters\n * DRYRUN: The default setting is False . If set to True, the protocol will be in dry run testing mode. The pipette will return the tip to the tiprack after each liquid transfer.\n * TEST_MODE_BEADS: The default setting is False . If set to True, the protocol will be in beads testing mode. The beads incubation and magnet engaging time will be in unit of seconds rather than minutes. Meanwhile, the pipette will return the tip to the tiprack after each liquid transfer.\n Timer parameters\n * timer_h: Set up the time for hours\n * timer_m: Set up the time for minutes\n Flow rate parameters\n * water_rate: Set up the flow rate of transferring water liquids, unit: folds of the default speed, 1.2 means 120 % of the default speed while 0.6 indicates 60% of the default speed\n * buffer_mmx_primer_rate: Set up the flow rate of transferring buffer/mastermix/primer liquids, unit: the same as above\n * sample_rate: Set up the flow rate of transferring sample-related liquids, unit: folds of the default speed\n * beads_rate: Set up the flow rate of transferring bead liquids, unit: the same as above\n * ethanol: Set up the flow rate of transferring ethanol liquids, unit: the same as above\n beads mixing parameters\n * beads_mix_reps: The frequencies that robot will mix the beads\n * beads_mix_rate: The flow rate that the robot will mix the beads, the same as Flow rate parameters\n* Magnetic Module parameters\n * magdeck_engage_height: The height of magnet that will engage, in mm\n * ethnaol_dis_zoffset: The height of dispensing ethanol from the top of the well during ethanol washing, in mm\n * incubation_time: The time it takes for DNA binding before engaging the magnet, unit in minutes when TEST_MODE_BEADS is False\n * beads_engaging_time: The time it takes for beads binding after engaging the magnet, unit in minutes when TEST_MODE_BEADS is False\n * airdry_time: The time it takes for airdrying after removing the enthanol, unit in minutes when TEST_MODE_BEADS is False\n * ethanol_wash_time: The time it takes for ethanol washing after adding it in the well, unit in minutes when TEST_MODE_BEADS is False\n", "internal": "0eaeb5", "labware": "\nBio-Rad 96 Well Plate 200 uL PCR\nNEST 96 Deepwell Plate 2mL\nNEST 12-Well Reservoir, 15 mL\n", "markdown": { diff --git a/protoBuilds/0f4405/README.json b/protoBuilds/0f4405/README.json index 8b9be75e0..fa7491ba4 100644 --- a/protoBuilds/0f4405/README.json +++ b/protoBuilds/0f4405/README.json @@ -5,7 +5,7 @@ "NEBNext\u00ae Ultra\u2122 II DNA Library Prep Kit for Illumina\u00ae" ] }, - "deck-setup": " \nreservoir (slot 9):\n* column 1: EtOH\n* column 2: elution buffer\n* column 12: waste (loaded empty)\nThermocycler plate (slot 7, 8, 10, 11):\n* columns 1-3: DNA samples\nMagnetic Module plate (slot 1):\n* columns 1-6: beads\nTemperature Module plate (slot 3):\n* column 1: mastermix 1\n* column 2: adaptor\n* column 3: mastermix 2\n* column 4: USER\n* columns 5-7: final PCR reagents\n", + "deck-setup": " \nreservoir (slot 9):\n column 1: EtOH\n column 2: elution buffer\n* column 12: waste (loaded empty)\nThermocycler plate (slot 7, 8, 10, 11):\n* columns 1-3: DNA samples\nMagnetic Module plate (slot 1):\n* columns 1-6: beads\nTemperature Module plate (slot 3):\n column 1: mastermix 1\n column 2: adaptor\n column 3: mastermix 2\n column 4: USER\n* columns 5-7: final PCR reagents\n", "description": "This protocol performs the NEBNext\u00ae Ultra\u2122 II DNA Library Prep Kit for Illumina\u00ae. The protocol includes a fully automated End Repair PCR step on the Opentrons Thermocycler. Up to 24 samples can be processed in one protocol run without the need to replenish tipracks or change out labware.\n", "internal": "0f4405", "labware": "\nEppendorf twin.tec \u00ae PCR Plate 96 #0030128648\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 96-Well Aluminum Block\nOpentrons 20\u00b5L Filter Tips\nOpentrons 200\u00b5L Filter Tips\n", diff --git a/protoBuilds/0f5985/README.json b/protoBuilds/0f5985/README.json index 43e3eb82b..9bae0a731 100644 --- a/protoBuilds/0f5985/README.json +++ b/protoBuilds/0f5985/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates the GenFind V3 protocol from Beckman Coulter for DNA isolation from whole blood or serum with magnetic particles. This protocol utilizes a P300-Multi channel pipette Gen2 (and optionally a p300-Single channel pipette Gen2) and gives the user the option to select a variable number of samples (Ideally a multiple of 8 for efficient use of reagents) and whether to dispense liquid waste in a 1-well reservoir in slot 6 or in the fixed trash container. The user can also choose whether they want to use Proteinase K and elution buffer from a tube-rack rather than the 12 well reservoir. \u00dfThis protocol is designed for holding the samples on the USA Scientific PlateOne\u00ae Deep 96-Well 2 mL Polypropylene Plate (P/N 1896-2800) on a 2nd generation Magnetic module. The purified samples are transferred to a Abgene\u2122 96 Well 0.8mL Polypropylene Deepwell Storage Plate (Thermo AB-0859) in the final step. The protocol uses the NEST 12 Well Reservoir 15 mL and the NEST 1 Well Reservoir 195 mL as sources of reagents. All reagents except the two wash buffers (Wash WBB and Wash WBC are stored either in the twelve well reservoir or the tube rack)\nThe protocol is broken down into 5 main parts:\n* Lysis buffer and proteinase K is added to the samples. The protocol is paused and the samples are incubated until the user is ready to continue. The pause allows the user to resuspend the magnetic particles in Bind BBB before adding the solution to the twelve well reservoir.\n* Bind BBB is added and the samples are incubated in order to bind DNA in the lysed solution.\n* The supernatant is discarded and the beads are washed two times with Wash WBB and two times with Wash WBC buffers.\n* Elution buffer is added to the samples which are then incubated and mixed two times.\n* Finally the supernatants containing DNA are transferred to the target plate.\nExplanation of parameters below:\n* Number of samples: How many samples to run, it should ideally be a multiple of 8 for efficient use of resources.\n* Blood cells or serum?: Choose what kind of samples to use for the protocol. This parameter will set the sample volume to 200 uL for blood cells, and 400 for serum samples. It will also set the elution volume to 200 uL for blood cell samples, and 40 uL for serum samples.\nThis setting will affect the volume requirements for all other reagents as well since they are all based on the starting volume.\n* x offset for bead aspiration: How many millimeters away from the center of the sample wells to aspirate bead supernatant from in the x (left/right) direction, the default is 1 mm.\n* Magnet extension (mm): How far from the base of the sample plate to extend the magnets of the magnet deck (default is 4.7 mm)\n* Proteinase K location: Choose whether the proteinase K is located in tube 1 of the tube rack, or well 1 of the 12 well reservoir\n* Elution buffer location: Choose whether the elution buffer is located in tube 2 to 8 of the tube rack, or well 6 and 7 of the 12 well reservoir\n* Liquid waste reservoir?: If set to yes the protocol will use a NEST 1 well 195 mL reservoir as a target of liquid waste, otherwise it will empty liquid waste into the regular trash bin. \n", + "description": "This protocol automates the GenFind V3 protocol from Beckman Coulter for DNA isolation from whole blood or serum with magnetic particles. This protocol utilizes a P300-Multi channel pipette Gen2 (and optionally a p300-Single channel pipette Gen2) and gives the user the option to select a variable number of samples (Ideally a multiple of 8 for efficient use of reagents) and whether to dispense liquid waste in a 1-well reservoir in slot 6 or in the fixed trash container. The user can also choose whether they want to use Proteinase K and elution buffer from a tube-rack rather than the 12 well reservoir. \u00dfThis protocol is designed for holding the samples on the USA Scientific PlateOne\u00ae Deep 96-Well 2 mL Polypropylene Plate (P/N 1896-2800) on a 2nd generation Magnetic module. The purified samples are transferred to a Abgene\u2122 96 Well 0.8mL Polypropylene Deepwell Storage Plate (Thermo AB-0859) in the final step. The protocol uses the NEST 12 Well Reservoir 15 mL and the NEST 1 Well Reservoir 195 mL as sources of reagents. All reagents except the two wash buffers (Wash WBB and Wash WBC are stored either in the twelve well reservoir or the tube rack)\nThe protocol is broken down into 5 main parts:\n Lysis buffer and proteinase K is added to the samples. The protocol is paused and the samples are incubated until the user is ready to continue. The pause allows the user to resuspend the magnetic particles in Bind BBB before adding the solution to the twelve well reservoir.\n Bind BBB is added and the samples are incubated in order to bind DNA in the lysed solution.\n The supernatant is discarded and the beads are washed two times with Wash WBB and two times with Wash WBC buffers.\n Elution buffer is added to the samples which are then incubated and mixed two times.\n* Finally the supernatants containing DNA are transferred to the target plate.\nExplanation of parameters below:\n Number of samples: How many samples to run, it should ideally be a multiple of 8 for efficient use of resources.\n Blood cells or serum?: Choose what kind of samples to use for the protocol. This parameter will set the sample volume to 200 uL for blood cells, and 400 for serum samples. It will also set the elution volume to 200 uL for blood cell samples, and 40 uL for serum samples.\nThis setting will affect the volume requirements for all other reagents as well since they are all based on the starting volume.\n x offset for bead aspiration: How many millimeters away from the center of the sample wells to aspirate bead supernatant from in the x (left/right) direction, the default is 1 mm.\n Magnet extension (mm): How far from the base of the sample plate to extend the magnets of the magnet deck (default is 4.7 mm)\n Proteinase K location: Choose whether the proteinase K is located in tube 1 of the tube rack, or well 1 of the 12 well reservoir\n Elution buffer location: Choose whether the elution buffer is located in tube 2 to 8 of the tube rack, or well 6 and 7 of the 12 well reservoir\n* Liquid waste reservoir?: If set to yes the protocol will use a NEST 1 well 195 mL reservoir as a target of liquid waste, otherwise it will empty liquid waste into the regular trash bin. \n", "internal": "0f5985", "labware": "\nNEST 1 Well Reservoir 195 mL\nNEST 12 Well Reservoir 15 mL\nUSA Scientific PlateOne\u00ae Deep 96-Well 2 mL Polypropylene Plate (P/N 1896-2800)\nAbgene\u2122 96 Well 0.8mL Polypropylene Deepwell Storage Plate (Thermo AB-0859)\n", "markdown": { diff --git a/protoBuilds/0fa015/README.json b/protoBuilds/0fa015/README.json index e4d91f58f..5be096f59 100644 --- a/protoBuilds/0fa015/README.json +++ b/protoBuilds/0fa015/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol fillsNEST 96-Well PCR Plate with QE using a GEN2 Multi-Channel Pipette.\n\nThe protocol can fill up to 9 plates and will dispense 10\u00b5L of QE into each well\n\nThis protocol is based largely on this protocol and will employ similar behaviors (touch tip after aspiration, blow out, and aspiration at the top of the well to prevent cross-contamination).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir\nNEST 96-Well PCR Plate\nReagents (QE)\n\n\n\nSlots 1 - 9: NEST 96-Well PCR Plate\nSlot 10: Opentrons Tips\nSlot 11: NEST 12-Well Reservoir\nA1: QE (for plates 1-5)\nA2: QE (for plates 6-9)\n\n\nUsing the customizations field (below), set up your protocol.\n* Pipette Type: Select which GEN2 Multi-Channel Pipette (p300 or p20) will be used\n* Pipette Mount: Select which mount (left or right) the Multi-Channel Pipette is attached to\n* Number of Plates (1-9): Specify the number of plates to fill", + "description": "This protocol fillsNEST 96-Well PCR Plate with QE using a GEN2 Multi-Channel Pipette.\n\nThe protocol can fill up to 9 plates and will dispense 10\u00b5L of QE into each well\n\nThis protocol is based largely on this protocol and will employ similar behaviors (touch tip after aspiration, blow out, and aspiration at the top of the well to prevent cross-contamination).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir\nNEST 96-Well PCR Plate\nReagents (QE)\n\n\n\nSlots 1 - 9: NEST 96-Well PCR Plate\nSlot 10: Opentrons Tips\nSlot 11: NEST 12-Well Reservoir\nA1: QE (for plates 1-5)\nA2: QE (for plates 6-9)\n\n\nUsing the customizations field (below), set up your protocol.\n Pipette Type: Select which GEN2 Multi-Channel Pipette (p300 or p20) will be used\n Pipette Mount: Select which mount (left or right) the Multi-Channel Pipette is attached to\n* Number of Plates (1-9): Specify the number of plates to fill", "internal": "0fa015", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/0ff0c3/README.json b/protoBuilds/0ff0c3/README.json index 890da006e..34617c96c 100644 --- a/protoBuilds/0ff0c3/README.json +++ b/protoBuilds/0ff0c3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n", - "description": "This is a Nucleaic Acid Purification Protocol for the OT-2 liquid handling system\nThe protocol is broken down into 3 main parts:\n* Pipette mixing of lysates, binding buffer and magnetic beads\n* Bead washing 3x using magnetic module\n* Final elution to PCR plate\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 6) to the elution PCR plate (slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\n", + "description": "This is a Nucleaic Acid Purification Protocol for the OT-2 liquid handling system\nThe protocol is broken down into 3 main parts:\n Pipette mixing of lysates, binding buffer and magnetic beads\n Bead washing 3x using magnetic module\n* Final elution to PCR plate\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 6) to the elution PCR plate (slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\n", "internal": "0ff0c3", "labware": "\nOT-2 Filter Tips, 200\u00b5L\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nNEST 1-Well Reservoir, 195 mL\n\nOpentrons Tough 0.2 mL 96-Well PCR Plate, Full Skirt\n", "markdown": { diff --git a/protoBuilds/10bf60-station-B/README.json b/protoBuilds/10bf60-station-B/README.json index b0b45a606..5d16904b8 100644 --- a/protoBuilds/10bf60-station-B/README.json +++ b/protoBuilds/10bf60-station-B/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This is a flexible protocol accommodating a wide range of commercial RNA extraction workflows for COVID-19 sample processing. The protocol is broken down into 5 main parts:\n* binding buffer addition to samples\n* bead wash 2x using magnetic module\n* final elution to chilled PCR strips\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nOpentrons temperature module\nNEST 12 Well Reservoir 15 mL or USA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 96 Deepwell Plate 2mL or USA Scientific 96 Deep Well Plate 2.4 mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 5\nReservoir 2: slot 2 (12mL per channel for full 96-sample run)\n\n", + "description": "This is a flexible protocol accommodating a wide range of commercial RNA extraction workflows for COVID-19 sample processing. The protocol is broken down into 5 main parts:\n binding buffer addition to samples\n bead wash 2x using magnetic module\n* final elution to chilled PCR strips\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nOpentrons temperature module\nNEST 12 Well Reservoir 15 mL or USA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 96 Deepwell Plate 2mL or USA Scientific 96 Deep Well Plate 2.4 mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 5\nReservoir 2: slot 2 (12mL per channel for full 96-sample run)\n\n", "internal": "10bf60", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/111210-part-10/README.json b/protoBuilds/111210-part-10/README.json index 6c782220d..172029ae6 100644 --- a/protoBuilds/111210-part-10/README.json +++ b/protoBuilds/111210-part-10/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the starting deck layout for Part 6 (Cleanup of Universal PCR with QIAact Beads).\n\n", - "description": "This protocol automates the tenth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* Magnetic Module Engage Height (mm): The height the magnets should raise.\n", + "description": "This protocol automates the tenth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n Magnetic Module Engage Height (mm): The height the magnets should raise.\n", "internal": "111210-part-10", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-2/README.json b/protoBuilds/111210-part-2/README.json index 8b34b9d79..39471ab76 100644 --- a/protoBuilds/111210-part-2/README.json +++ b/protoBuilds/111210-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the deck layout when the samples are placed in 1.5 mL Screwcap tubes in an Opentrons Tube Rack.\n\n", - "description": "This protocol automates the second part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Reverse transcription part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", + "description": "This protocol automates the second part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Reverse transcription part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", "internal": "111210-part-2", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-3/README.json b/protoBuilds/111210-part-3/README.json index d9c58701a..e40131d92 100644 --- a/protoBuilds/111210-part-3/README.json +++ b/protoBuilds/111210-part-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the deck layout when the samples are placed in 1.5 mL Screwcap tubes in an Opentrons Tube Rack.\n\n", - "description": "This protocol automates the third part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Second strand synthesis part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", + "description": "This protocol automates the third part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Second strand synthesis part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", "internal": "111210-part-3", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-4/README.json b/protoBuilds/111210-part-4/README.json index de470befb..c5f8488a1 100644 --- a/protoBuilds/111210-part-4/README.json +++ b/protoBuilds/111210-part-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates the fourth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the End repair / dA tailing part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", + "description": "This protocol automates the fourth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the End repair / dA tailing part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", "internal": "111210-part-4", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-5/README.json b/protoBuilds/111210-part-5/README.json index a41b03393..e3516772a 100644 --- a/protoBuilds/111210-part-5/README.json +++ b/protoBuilds/111210-part-5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates the fifth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Adaptor ligation part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", + "description": "This protocol automates the fifth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Adaptor ligation part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", "internal": "111210-part-5", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-6/README.json b/protoBuilds/111210-part-6/README.json index 5ab127946..96598c3a5 100644 --- a/protoBuilds/111210-part-6/README.json +++ b/protoBuilds/111210-part-6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates the sixth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Adapter-ligated DNA with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* Magnetic Module Engage Height: The height the magnets should raise.\n", + "description": "This protocol automates the sixth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Adapter-ligated DNA with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n Magnetic Module Engage Height: The height the magnets should raise.\n", "internal": "111210-part-6", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-7/README.json b/protoBuilds/111210-part-7/README.json index 90c9b806d..3e740f471 100644 --- a/protoBuilds/111210-part-7/README.json +++ b/protoBuilds/111210-part-7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the starting deck layout for Part 4 (Target Enrichment PCR).\n\n", - "description": "This protocol automates the seventh part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Target Enrichment PCR part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", + "description": "This protocol automates the seventh part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Target Enrichment PCR part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", "internal": "111210-part-7", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-8/README.json b/protoBuilds/111210-part-8/README.json index 321bc989d..d68f5df04 100644 --- a/protoBuilds/111210-part-8/README.json +++ b/protoBuilds/111210-part-8/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the starting deck layout for Part 5 (Cleanup of Target Enrichment PCR with QIAact Beads).\n\n", - "description": "This protocol automates the eigth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* Magnetic Module Engage Height (mm): The height the magnets should raise.\n", + "description": "This protocol automates the eigth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n Magnetic Module Engage Height (mm): The height the magnets should raise.\n", "internal": "111210-part-8", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210-part-9/README.json b/protoBuilds/111210-part-9/README.json index 2ec9097ef..50b56aa46 100644 --- a/protoBuilds/111210-part-9/README.json +++ b/protoBuilds/111210-part-9/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the starting deck layout for Part 6 (Universal PCR Amplification).\n\n", - "description": "This protocol automates the ninth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", + "description": "This protocol automates the ninth part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAseq Beads part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", "internal": "111210-part-9", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/111210/README.json b/protoBuilds/111210/README.json index 1acc19b0f..1f16e9500 100644 --- a/protoBuilds/111210/README.json +++ b/protoBuilds/111210/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the deck layout when the samples are placed in 1.5 mL Screwcap tubes in an Opentrons Tube Rack.\n\n", - "description": "This protocol automates the first part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the First strand cDNA synthesis part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* Samples Labware Type: The starting samples can be placed in either 1.5 mL tubes on the Opentrons Tube Rack OR in a 96 Well Plate.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", + "description": "This protocol automates the first part of a ten part protocol for the GeneRead QIAact Lung RNA Fusion UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the First strand cDNA synthesis part described in the GeneRead QIAact Lung RNA Fusion UMI Panel Handbook.\n\nPart 1: GeneRead QIAact Lung RNA Fusion UMI\nPart 2: Reverse transcription\nPart 3: Second strand synthesis\nPart 4: End repair / dA tailing\nPart 5: Adaptor ligation\nPart 6: Cleanup of Adapter-ligated DNA with QIAseq Beads\nPart 7: Target Enrichment PCR\nPart 8: Cleanup of Target Enrichment PCR with QIAseq Beads\nPart 9: Universal PCR Amplification\nPart 10: Cleanup of Universal PCR with QIAseq Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n Samples Labware Type: The starting samples can be placed in either 1.5 mL tubes on the Opentrons Tube Rack OR in a 96 Well Plate.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n", "internal": "111210", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/115d98/README.json b/protoBuilds/115d98/README.json index 9e77c8bb5..bb2e40472 100644 --- a/protoBuilds/115d98/README.json +++ b/protoBuilds/115d98/README.json @@ -5,7 +5,7 @@ "Aliquoting" ] }, - "description": "This flexible protocol automates the transferring of samples in 12mL tubes to dilution buffer, then to Visby device for rapid Covid testing.\n\n\n\nProtocol Steps\n1. The protocol begins by transferring (up to 5) samples from row A in slot 2 to A1, A3, A5, C1 and C3 (in that order) in slot 5, containing dilution buffer.\n2. Once all samples are transferred to dilution buffer, total volume of samples will be added from slot 5 to Visby.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nP1000 Single-Channel GEN2\nOpentrons 1000\u00b5L Filter Tips\nVisby Device with Adapter\nCustom Tube Rack with 12mL Tubes\n\n\n\n\nDeck Layout\n\nSlot 1: Opentrons 1000\u00b5L Filter Tips\n\nSlot 2: Custom Tube Rack with 12mL Tubes, containing samples in row A\n\nSlot 5: Custom Tube Rack with 12mL Tubes, cotaining dilution buffer in A1, A3, A5, C1, and C3 (depending on the number of samples)\n\nSlot 7: Visby 3\n\nSlot 8: Visby 4\n\nSlot 9: Visby 5\n\nSlot 10: Visby 1\n\nSlot 11: Visby 2\n\n\nExplanation of adjustable parameters below:\n* P1000 Single GEN2 Mount: Select which mount (left, right) the pipette is attached to.\n* Sample Volume (\u00b5L): Specify the volume (in \u00b5L) that should be transferred to the Visby. This volume will be transferred to the dilution buffer, before being transferred to the Visby.\n* Number of Samples: Select the number of samples to test (1-5).", + "description": "This flexible protocol automates the transferring of samples in 12mL tubes to dilution buffer, then to Visby device for rapid Covid testing.\n\n\n\nProtocol Steps\n1. The protocol begins by transferring (up to 5) samples from row A in slot 2 to A1, A3, A5, C1 and C3 (in that order) in slot 5, containing dilution buffer.\n2. Once all samples are transferred to dilution buffer, total volume of samples will be added from slot 5 to Visby.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nP1000 Single-Channel GEN2\nOpentrons 1000\u00b5L Filter Tips\nVisby Device with Adapter\nCustom Tube Rack with 12mL Tubes\n\n\n\n\nDeck Layout\n\nSlot 1: Opentrons 1000\u00b5L Filter Tips\n\nSlot 2: Custom Tube Rack with 12mL Tubes, containing samples in row A\n\nSlot 5: Custom Tube Rack with 12mL Tubes, cotaining dilution buffer in A1, A3, A5, C1, and C3 (depending on the number of samples)\n\nSlot 7: Visby 3\n\nSlot 8: Visby 4\n\nSlot 9: Visby 5\n\nSlot 10: Visby 1\n\nSlot 11: Visby 2\n\n\nExplanation of adjustable parameters below:\n P1000 Single GEN2 Mount: Select which mount (left, right) the pipette is attached to.\n Sample Volume (\u00b5L): Specify the volume (in \u00b5L) that should be transferred to the Visby. This volume will be transferred to the dilution buffer, before being transferred to the Visby.\n* Number of Samples: Select the number of samples to test (1-5).", "internal": "115d98", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/11bb6a-part-3/README.json b/protoBuilds/11bb6a-part-3/README.json index 9379619b3..ce0103d44 100644 --- a/protoBuilds/11bb6a-part-3/README.json +++ b/protoBuilds/11bb6a-part-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons Temperature Module with dropdown-selected aluminum block and tube combination \n\n\n\nSlot 3: Library Prep Plate (dropdown-selected 96-well PCR plate) \nSlot 6: Reagent Plate (dropdown-selected 96-well PCR plate) \nSlot 9: Magnetic Module with dropdown-selected 96-well PCR plate \nSlot 8: Opentrons 200 uL filter tips \nSlots 7, 10, 11: Opentrons 20 uL filter tips \n", - "description": "This protocol uses multi-channel P20 and P300 pipettes to perform end prep steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate, the reagent plate, and the 96-well PCR plate on the magnetic module and the labware for reagent tubes on the temperature module.\nLinks:\n* Part 1: Enzymatic Fragmentation and End Prep\n* Part 2: Sample Cleanup for Covaris Samples\n* Part 3: End Prep\n* Part 4: Adapter Ligation\n* Part 5: Size Selection\n* Part 6: Clean Up\n* Part 7: PCR Enrichment\n* Part 8: Sample Clean Up\n* Part 9: Fragment Analyzer\n* Part 10: Pooling According to Concentration\n", + "description": "This protocol uses multi-channel P20 and P300 pipettes to perform end prep steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate, the reagent plate, and the 96-well PCR plate on the magnetic module and the labware for reagent tubes on the temperature module.\nLinks:\n Part 1: Enzymatic Fragmentation and End Prep\n Part 2: Sample Cleanup for Covaris Samples\n Part 3: End Prep\n Part 4: Adapter Ligation\n Part 5: Size Selection\n Part 6: Clean Up\n Part 7: PCR Enrichment\n Part 8: Sample Clean Up\n Part 9: Fragment Analyzer\n Part 10: Pooling According to Concentration\n", "internal": "11bb6a-part-3", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons Temperature Module] (https://shop.opentrons.com/modules/)\n[Opentrons Magnetic Module] (https://shop.opentrons.com/modules/)\n[Selected 96-well PCR plate] ([see parameter dropdown list below] https://labware.opentrons.com/)\n[Selected aluminum block and tube combination] ([see parameter dropdown list below] https://labware.opentrons.com/)\n", "markdown": { diff --git a/protoBuilds/11bb6a-part-4/README.json b/protoBuilds/11bb6a-part-4/README.json index 897592096..3b7e95ac1 100644 --- a/protoBuilds/11bb6a-part-4/README.json +++ b/protoBuilds/11bb6a-part-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons Temperature Module with dropdown-selected aluminum block and tube combination \n\n\n\nSlot 3: Library Prep Plate (dropdown-selected 96-well PCR plate) \nSlot 6: Reagent Plate (dropdown-selected 96-well PCR plate) \nSlot 9: Magnetic Module empty \nSlot 8: Opentrons 200 uL filter tips \nSlots 7, 10, 11: Opentrons 20 uL filter tips \n", - "description": "This protocol uses multi-channel P20 and P300 pipettes to perform adapter ligation steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate, the reagent plate, and the labware for reagent tubes on the temperature module.\nLinks:\n* Part 1: Enzymatic Fragmentation and End Prep\n* Part 2: Sample Cleanup for Covaris Samples\n* Part 3: End Prep\n* Part 4: Adapter Ligation\n* Part 5: Size Selection\n* Part 6: Clean Up\n* Part 7: PCR Enrichment\n* Part 8: Sample Clean Up\n* Part 9: Fragment Analyzer\n* Part 10: Pooling According to Concentration\n", + "description": "This protocol uses multi-channel P20 and P300 pipettes to perform adapter ligation steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate, the reagent plate, and the labware for reagent tubes on the temperature module.\nLinks:\n Part 1: Enzymatic Fragmentation and End Prep\n Part 2: Sample Cleanup for Covaris Samples\n Part 3: End Prep\n Part 4: Adapter Ligation\n Part 5: Size Selection\n Part 6: Clean Up\n Part 7: PCR Enrichment\n Part 8: Sample Clean Up\n Part 9: Fragment Analyzer\n Part 10: Pooling According to Concentration\n", "internal": "11bb6a-part-4", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons Temperature Module] (https://shop.opentrons.com/modules/)\n[Selected 96-well PCR plate] ([see parameter dropdown list below] https://labware.opentrons.com/)\n[Selected aluminum block and tube combination] ([see parameter dropdown list below] https://labware.opentrons.com/)\n", "markdown": { diff --git a/protoBuilds/11bb6a-part-5/README.json b/protoBuilds/11bb6a-part-5/README.json index ac2764003..c2bbc36be 100644 --- a/protoBuilds/11bb6a-part-5/README.json +++ b/protoBuilds/11bb6a-part-5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons Temperature Module empty \nSlot 3: Size Plate (dropdown-selected 96-well PCR plate) \nSlot 5: Reagent Reservoir (Nest 12-well 15 mL reservoir) \n\n\n\nSlot 6: Ethanol (Agilent 290 mL reservoir) \nSlot 8: Liquid Waste (Agilent 290 mL reservoir) \nSlot 9: Opentrons Magnetic Module with library prep plate (dropdown-selected 96-well PCR plate) \nSlot 10: Opentrons 20 uL filter tips \nSlots 2,4,7,11: Opentrons 200 uL filter tips \n", - "description": "This protocol uses multi-channel P20 and P300 pipettes to perform size selection steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate and the size plate.\nLinks:\n* Part 1: Enzymatic Fragmentation and End Prep\n* Part 2: Sample Cleanup for Covaris Samples\n* Part 3: End Prep\n* Part 4: Adapter Ligation\n* Part 5: Size Selection\n* Part 6: Clean Up\n* Part 7: PCR Enrichment\n* Part 8: Sample Clean Up\n* Part 9: Fragment Analyzer\n* Part 10: Pooling According to Concentration\n", + "description": "This protocol uses multi-channel P20 and P300 pipettes to perform size selection steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate and the size plate.\nLinks:\n Part 1: Enzymatic Fragmentation and End Prep\n Part 2: Sample Cleanup for Covaris Samples\n Part 3: End Prep\n Part 4: Adapter Ligation\n Part 5: Size Selection\n Part 6: Clean Up\n Part 7: PCR Enrichment\n Part 8: Sample Clean Up\n Part 9: Fragment Analyzer\n Part 10: Pooling According to Concentration\n", "internal": "11bb6a-part-5", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons Temperature Module] (https://shop.opentrons.com/modules/)\n[Opentrons Magnetic Module] (https://shop.opentrons.com/modules/)\n[Selected 96-well PCR plate] ([see parameter dropdown list below] https://labware.opentrons.com/)\n", "markdown": { diff --git a/protoBuilds/11bb6a-part-6/README.json b/protoBuilds/11bb6a-part-6/README.json index 40b4e0530..d9384f4d5 100644 --- a/protoBuilds/11bb6a-part-6/README.json +++ b/protoBuilds/11bb6a-part-6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons Temperature Module empty \nSlot 5: Reagent Reservoir (Nest 12-well 15 mL reservoir) \n\n\n\nSlot 6: Ethanol (Agilent 290 mL reservoir) \nSlot 8: Liquid Waste (Agilent 290 mL reservoir) \nSlot 9: Opentrons Magnetic Module with library prep plate (dropdown-selected 96-well PCR plate) \nSlot 10: Opentrons 20 uL filter tips \nSlots 2,4,7,11: Opentrons 200 uL filter tips \n", - "description": "This protocol uses multi-channel P20 and P300 pipettes to perform bead cleanup steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate and the size plate.\nLinks:\n* Part 1: Enzymatic Fragmentation and End Prep\n* Part 2: Sample Cleanup for Covaris Samples\n* Part 3: End Prep\n* Part 4: Adapter Ligation\n* Part 5: Size Selection\n* Part 6: Clean Up\n* Part 7: PCR Enrichment\n* Part 8: Sample Clean Up\n* Part 9: Fragment Analyzer\n* Part 10: Pooling According to Concentration\n", + "description": "This protocol uses multi-channel P20 and P300 pipettes to perform bead cleanup steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate and the size plate.\nLinks:\n Part 1: Enzymatic Fragmentation and End Prep\n Part 2: Sample Cleanup for Covaris Samples\n Part 3: End Prep\n Part 4: Adapter Ligation\n Part 5: Size Selection\n Part 6: Clean Up\n Part 7: PCR Enrichment\n Part 8: Sample Clean Up\n Part 9: Fragment Analyzer\n Part 10: Pooling According to Concentration\n", "internal": "11bb6a-part-6", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons Temperature Module] (https://shop.opentrons.com/modules/)\n[Opentrons Magnetic Module] (https://shop.opentrons.com/modules/)\n[Selected 96-well PCR plate] ([see parameter dropdown list below] https://labware.opentrons.com/)\n", "markdown": { diff --git a/protoBuilds/11bb6a-part-7/README.json b/protoBuilds/11bb6a-part-7/README.json index ba39d00e9..8e599b1d4 100644 --- a/protoBuilds/11bb6a-part-7/README.json +++ b/protoBuilds/11bb6a-part-7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons Temperature Module (dropdown-selected aluminum block and tube combination) \n\n\n\nSlot 2: i5 indexes (eppendorf_96_wellplate_200ul) \nSlot 5: i7 indexes (eppendorf_96_wellplate_200ul) \nSlot 8: PCR plate (dropdown-selected 96-well PCR plate) \nSlot 9: Opentrons Magnetic Module with library prep plate or size plate (dropdown-selected 96-well PCR plate) \nSlots 10,3,6: Opentrons 20 uL filter tips \nSlot 11: Opentrons 200 uL filter tips \n", - "description": "This protocol uses multi-channel P20 and P300 pipettes to perform PCR enrichment setup steps on 48-96 input samples. User-determined parameters are available for selection of the i7 primer plate row, the i5 primer plate column, sample count, and labware.\nLinks:\n* Part 1: Enzymatic Fragmentation and End Prep\n* Part 2: Sample Cleanup for Covaris Samples\n* Part 3: End Prep\n* Part 4: Adapter Ligation\n* Part 5: Size Selection\n* Part 6: Clean Up\n* Part 7: PCR Enrichment\n* Part 8: Sample Clean Up\n* Part 9: Fragment Analyzer\n* Part 10: Pooling According to Concentration\n", + "description": "This protocol uses multi-channel P20 and P300 pipettes to perform PCR enrichment setup steps on 48-96 input samples. User-determined parameters are available for selection of the i7 primer plate row, the i5 primer plate column, sample count, and labware.\nLinks:\n Part 1: Enzymatic Fragmentation and End Prep\n Part 2: Sample Cleanup for Covaris Samples\n Part 3: End Prep\n Part 4: Adapter Ligation\n Part 5: Size Selection\n Part 6: Clean Up\n Part 7: PCR Enrichment\n Part 8: Sample Clean Up\n Part 9: Fragment Analyzer\n Part 10: Pooling According to Concentration\n", "internal": "11bb6a-part-7", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons Temperature Module] (https://shop.opentrons.com/modules/)\n[Opentrons Magnetic Module] (https://shop.opentrons.com/modules/)\n[Selected 96-well PCR plate] ([see parameter dropdown list below] https://labware.opentrons.com/)\n", "markdown": { diff --git a/protoBuilds/11bb6a-part-8/README.json b/protoBuilds/11bb6a-part-8/README.json index 3a4eed31e..284715001 100644 --- a/protoBuilds/11bb6a-part-8/README.json +++ b/protoBuilds/11bb6a-part-8/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons Temperature Module empty \nSlot 3: Output Plate (dropdown selected 96-well PCR plate) \nSlot 5: Reagent Reservoir (Nest 12-well 15 mL reservoir) \n\n\n\nSlot 6: Ethanol (Agilent 290 mL reservoir) \nSlot 8: Liquid Waste (Agilent 290 mL reservoir) \nSlot 9: Opentrons Magnetic Module with PCR plate (dropdown-selected 96-well PCR plate) \nSlots 10,11: Opentrons 20 uL filter tips \nSlots 2,4,7: Opentrons 200 uL filter tips \n", - "description": "This protocol uses multi-channel P20 and P300 pipettes to perform bead cleanup steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate and the output plate.\nLinks:\n* Part 1: Enzymatic Fragmentation and End Prep\n* Part 2: Sample Cleanup for Covaris Samples\n* Part 3: End Prep\n* Part 4: Adapter Ligation\n* Part 5: Size Selection\n* Part 6: Clean Up\n* Part 7: PCR Enrichment\n* Part 8: Sample Clean Up\n* Part 9: Fragment Analyzer\n* Part 10: Pooling According to Concentration\n", + "description": "This protocol uses multi-channel P20 and P300 pipettes to perform bead cleanup steps on 48-96 input samples. User-determined parameters are available for selection of the labware for the library prep plate and the output plate.\nLinks:\n Part 1: Enzymatic Fragmentation and End Prep\n Part 2: Sample Cleanup for Covaris Samples\n Part 3: End Prep\n Part 4: Adapter Ligation\n Part 5: Size Selection\n Part 6: Clean Up\n Part 7: PCR Enrichment\n Part 8: Sample Clean Up\n Part 9: Fragment Analyzer\n Part 10: Pooling According to Concentration\n", "internal": "11bb6a-part-8", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons Temperature Module] (https://shop.opentrons.com/modules/)\n[Opentrons Magnetic Module] (https://shop.opentrons.com/modules/)\n[Selected 96-well PCR plate] ([see parameter dropdown list below] https://labware.opentrons.com/)\n", "markdown": { diff --git a/protoBuilds/11bb6a-part-9/README.json b/protoBuilds/11bb6a-part-9/README.json index 1fcc530ca..16fd9f0e7 100644 --- a/protoBuilds/11bb6a-part-9/README.json +++ b/protoBuilds/11bb6a-part-9/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 1: Opentrons Temperature Module empty \nSlot 3: Libraries Plate (dropdown selected 96-well PCR plate) \nSlot 5: Reagent Reservoir (Nest 12-well 15 mL reservoir) \nSlot 6: Fragment Analyzer Plate on Opentrons 96-Well Aluminum Block (biorad_96_fragment_analyzer_plate_aluminumblock_200ul) \nSlot 9: Opentrons Magnetic Module empty \nSlot 10: Opentrons 20 uL filter tips \nSlot 7: Opentrons 200 uL filter tips \n", - "description": "This protocol uses multi-channel P20 and P300 pipettes to perform fragment analyzer set up steps on 48-96 output libraries. User-determined parameters are available for selection of the labware for the libraries plate.\nLinks:\n* Part 1: Enzymatic Fragmentation and End Prep\n* Part 2: Sample Cleanup for Covaris Samples\n* Part 3: End Prep\n* Part 4: Adapter Ligation\n* Part 5: Size Selection\n* Part 6: Clean Up\n* Part 7: PCR Enrichment\n* Part 8: Sample Clean Up\n* Part 9: Fragment Analyzer\n* Part 10: Pooling According to Concentration\n", + "description": "This protocol uses multi-channel P20 and P300 pipettes to perform fragment analyzer set up steps on 48-96 output libraries. User-determined parameters are available for selection of the labware for the libraries plate.\nLinks:\n Part 1: Enzymatic Fragmentation and End Prep\n Part 2: Sample Cleanup for Covaris Samples\n Part 3: End Prep\n Part 4: Adapter Ligation\n Part 5: Size Selection\n Part 6: Clean Up\n Part 7: PCR Enrichment\n Part 8: Sample Clean Up\n Part 9: Fragment Analyzer\n Part 10: Pooling According to Concentration\n", "internal": "11bb6a-part-9", "labware": "\n[Opentrons Filter Tips for the P20 and P300] (https://shop.opentrons.com)\n[Opentrons Temperature Module] (https://shop.opentrons.com/modules/)\n[Opentrons Magnetic Module] (https://shop.opentrons.com/modules/)\n[Selected 96-well PCR plate] ([see parameter dropdown list below] https://labware.opentrons.com/)\n", "markdown": { diff --git a/protoBuilds/121d15-2-384/README.json b/protoBuilds/121d15-2-384/README.json index a31a6a13a..4a936c97c 100644 --- a/protoBuilds/121d15-2-384/README.json +++ b/protoBuilds/121d15-2-384/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n9\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n9,219\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n9\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,135,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,262\n7,242\n8,218\n9,219\n...\n", "internal": "121d15", "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 384 Well Plate 225 \u00b5L\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-2-96-Greiner-1000/README.json b/protoBuilds/121d15-2-96-Greiner-1000/README.json index 4a4bbf89e..d63f26c94 100644 --- a/protoBuilds/121d15-2-96-Greiner-1000/README.json +++ b/protoBuilds/121d15-2-96-Greiner-1000/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", "internal": "121d15", "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 96 Well Plate 500 \u00b5L\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-2-96-Greiner-500/README.json b/protoBuilds/121d15-2-96-Greiner-500/README.json index f24cc4e9b..1ef229587 100644 --- a/protoBuilds/121d15-2-96-Greiner-500/README.json +++ b/protoBuilds/121d15-2-96-Greiner-500/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", "internal": "121d15", "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 96 Well Plate 500 \u00b5L\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-2-96-Irish-2200/README.json b/protoBuilds/121d15-2-96-Irish-2200/README.json index c87475865..83d7eada4 100644 --- a/protoBuilds/121d15-2-96-Irish-2200/README.json +++ b/protoBuilds/121d15-2-96-Irish-2200/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom Redo Replacement Picking protocol from a worklist. The worklist should be specified as follows:\nNumber of Redo\n8\npos TB_RCK_1,pos MTP_1,disposal_vol,transfer_vol\nTUBE BAR,PLATE BAR\n1,1,200,200\n2,35,200,200\n3,2,150,200\n4,90,100,100\n5,84\n6,62\n7,42\n8,18\n...\n", "internal": "121d15", "labware": "\nCustom 48-tuberack\nGreiner MASTERBLOCK 96 Well Plate 500 \u00b5L\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-3/README.json b/protoBuilds/121d15-3/README.json index 412f53308..ee5bdeacc 100644 --- a/protoBuilds/121d15-3/README.json +++ b/protoBuilds/121d15-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom HPLC Picking protocol from a worklist. The worklist should be specified as follows:\nsource,dest,volume\n1,A1,300\n2,A1,300\n3,A1,300\n4,A1,300\n10,B1,300\n12,B1,300\n13,B1,300\n14,B1,\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom HPLC Picking protocol from a worklist. The worklist should be specified as follows:\nsource,dest,volume\n1,A1,300\n2,A1,300\n3,A1,300\n4,A1,300\n10,B1,300\n12,B1,300\n13,B1,300\n14,B1,\n", "internal": "121d15", "labware": "\nIrish Life Sciences 2.2mL Deep Well Plate, V-Bottom #2.2S96-008V\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-4/README.json b/protoBuilds/121d15-4/README.json index e8801add9..818932700 100644 --- a/protoBuilds/121d15-4/README.json +++ b/protoBuilds/121d15-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling elution for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling elution for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", "internal": "121d15", "labware": "\nCustom 96-tuberack\nNEST 1 Reservoir 195ml\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-5/README.json b/protoBuilds/121d15-5/README.json index 21ae3da9e..b1be7dd1c 100644 --- a/protoBuilds/121d15-5/README.json +++ b/protoBuilds/121d15-5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling and elution for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling and elution for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", "internal": "121d15", "labware": "\nCustom 96-tuberack\nNEST 1 Reservoir 195ml\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-6/README.json b/protoBuilds/121d15-6/README.json index b14c3a214..d0ecd9c61 100644 --- a/protoBuilds/121d15-6/README.json +++ b/protoBuilds/121d15-6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling and elution for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling and elution for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", "internal": "121d15", "labware": "\nCustom 96-tuberack\nNEST 1 Reservoir 195ml\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-7-2ml-15ml-aliquot/README.json b/protoBuilds/121d15-7-2ml-15ml-aliquot/README.json index 7af8ae960..12924aea6 100644 --- a/protoBuilds/121d15-7-2ml-15ml-aliquot/README.json +++ b/protoBuilds/121d15-7-2ml-15ml-aliquot/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom pooling protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom pooling protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", "internal": "121d15", "labware": "\nCustom 96-tuberacks\nOpentrons 4-in-1 Tube Rack Set with 3x5 15ml Tube Insert\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-7-2ml-15ml-pool/README.json b/protoBuilds/121d15-7-2ml-15ml-pool/README.json index 7af8ae960..12924aea6 100644 --- a/protoBuilds/121d15-7-2ml-15ml-pool/README.json +++ b/protoBuilds/121d15-7-2ml-15ml-pool/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom pooling protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom pooling protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", "internal": "121d15", "labware": "\nCustom 96-tuberacks\nOpentrons 4-in-1 Tube Rack Set with 3x5 15ml Tube Insert\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-7-2ml-2ml-aliquot/README.json b/protoBuilds/121d15-7-2ml-2ml-aliquot/README.json index 864cef244..396804910 100644 --- a/protoBuilds/121d15-7-2ml-2ml-aliquot/README.json +++ b/protoBuilds/121d15-7-2ml-2ml-aliquot/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom aliquoting protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom aliquoting protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", "internal": "121d15", "labware": "\nCustom 96-tuberacks\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-7-2ml-2ml-pool/README.json b/protoBuilds/121d15-7-2ml-2ml-pool/README.json index 9b915482f..83f704de9 100644 --- a/protoBuilds/121d15-7-2ml-2ml-pool/README.json +++ b/protoBuilds/121d15-7-2ml-2ml-pool/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom pooling protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom pooling protocol from a worklist. The worklist should be specified as follows:\nNumber\n8\npos TB_RCK_1,pos MTP_1,transfer_vol\nTUBE BAR 1,TUBE BAR 1\n1,1,200\n2,35,200\n3,2,150\n4,90,100\n5,84\n6,62\n7,42\n8,18\n...\n", "internal": "121d15", "labware": "\nCustom 96-tuberacks\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15-repeat/README.json b/protoBuilds/121d15-repeat/README.json index 51f8b9149..1e07a5bba 100644 --- a/protoBuilds/121d15-repeat/README.json +++ b/protoBuilds/121d15-repeat/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave with Repeat for 2nd EDA\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave with Repeat for 2nd EDA\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", "internal": "121d15-repeat", "labware": "\nCustom 96-tuberack\nNEST 1 Reservoir 195ml\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/121d15/README.json b/protoBuilds/121d15/README.json index fc51def3a..884039d91 100644 --- a/protoBuilds/121d15/README.json +++ b/protoBuilds/121d15/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Manual Cleave\n\n\n* Manual Cleave with Repeat for 2nd EDA\n\n\n* Manual Cleave Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n* Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n* HPLC Picking\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n* Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n* Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n* Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n* Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n* Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", + "description": "Links:\n Manual Cleave\n\n\n Manual Cleave with Repeat for 2nd EDA\n\n\n Manual Cleave Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (Off-deck Vacuum)\n\n\n Manual Cleave, ACN + Elution (On-deck Vacuum)\n\n\n HPLC Picking\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 500 \u00b5L)\n\n\n Redo Replacement Picking (Greiner MASTERBLOCK 96 Well Plate 1000 \u00b5L)\n\n\n Redo Replacement Picking (Irish Life Sciences 96 Well Plate 2200 \u00b5L)\n\n\n Redo Replacement Picking (Greiner Masterblock 384 Well Plate 225 \u00b5L)\n\n\n Aliquoting - 2ml Tuberack to 2ml Tuberack\n\n\n Aliquoting - 15ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 2ml Tuberack\n\n\n Pooling - 2ml Tuberack to 15ml Tuberack\n\n\nThis protocol performs a custom plate filling for up to 4x 96-well plates from a single reagent reservoir. The user can input the number of rows and columns to be filled for each plate. Liquid handling parameters are automatically determined from the user's selection of which reagent will be added during the run.\n", "internal": "121d15", "labware": "\nCustom 96-tuberack\nNEST 1 Reservoir 195ml\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/12213d/README.json b/protoBuilds/12213d/README.json index 7e777da8e..b2bf66910 100644 --- a/protoBuilds/12213d/README.json +++ b/protoBuilds/12213d/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol removes ethanol from a plate on the MagDeck and requires manual intervention by the user.\n\nAfter incubating on the MagDeck for 5 minutes, 150\u00b5L will be removed from each well. The user will then be prompted to remove the plate and centrifuge. After centrifuging, the user will replace the plate and a second incubation and liquid transfer will occur.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module\nOpentrons P300 Multi-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons P20 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nNEST 96-Well Plates\nUSA Scientific 12-Well Reservoir\n\n\n\nSlot 1: USA Scientific 12-Well Reservoir with ethanol in slots 1-4\nSlot 3: Opentrons 20\u00b5L Tips\nSlot 4: Opentrons Magnetic Module with NEST 96-Well Plates\nSlot 6: Opentrons 300\u00b5L Tips\n\n\nUsing the customizations field (below), set up your protocol.\n* P300-Multi Pipette Mount: Select which mount (left or right) the P300-Multi is attached to.\n* P20-Multi Pipette Mount: Select which mount (left or right) the P20-Multi is attached to.", + "description": "This protocol removes ethanol from a plate on the MagDeck and requires manual intervention by the user.\n\nAfter incubating on the MagDeck for 5 minutes, 150\u00b5L will be removed from each well. The user will then be prompted to remove the plate and centrifuge. After centrifuging, the user will replace the plate and a second incubation and liquid transfer will occur.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module\nOpentrons P300 Multi-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons P20 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nNEST 96-Well Plates\nUSA Scientific 12-Well Reservoir\n\n\n\nSlot 1: USA Scientific 12-Well Reservoir with ethanol in slots 1-4\nSlot 3: Opentrons 20\u00b5L Tips\nSlot 4: Opentrons Magnetic Module with NEST 96-Well Plates\nSlot 6: Opentrons 300\u00b5L Tips\n\n\nUsing the customizations field (below), set up your protocol.\n P300-Multi Pipette Mount: Select which mount (left or right) the P300-Multi is attached to.\n P20-Multi Pipette Mount: Select which mount (left or right) the P20-Multi is attached to.", "internal": "12213d", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/13ac78/README.json b/protoBuilds/13ac78/README.json index 393ee9874..a021506d8 100644 --- a/protoBuilds/13ac78/README.json +++ b/protoBuilds/13ac78/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "deck-setup": "\nReagents:\n* green: mastermix\n* blue: samples\n* pink: positive control\n* purple: molecular grade water\n", + "deck-setup": "\nReagents:\n green: mastermix\n blue: samples\n pink: positive control\n purple: molecular grade water\n", "description": "This protocol performs a custom PCR Prep from strip tubes seated in a custom cooling rack into a 384-well plate for up to 16 samples. The transfer scheme is follows:\n\n", "internal": "13ac78", "labware": "\nNEST PCR 8-Strip Tubes 0.2ml #403022 seated in SSbio IsoFreeze PCR Rack #5650-T4\nThermoFisher MicroAmp\u2122 Optical 384-Well Reaction Plate #4343370\nOpentrons 20uL Filter Tips\n", diff --git a/protoBuilds/13c0b8/README.json b/protoBuilds/13c0b8/README.json index db0802ec8..5d0b0e345 100644 --- a/protoBuilds/13c0b8/README.json +++ b/protoBuilds/13c0b8/README.json @@ -5,7 +5,7 @@ "Staining Prep" ] }, - "description": "This protocol performs the cell staining protocol as outlined in the 'Cell staining automation' document. This protocol uses a P20 Single (attached to the left mount) and a P300 (attached to the right mount).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Temperature Module\nOpentrons P20 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nOpentrons 300\u00b5L Tips\n96-Well BRANDplates with V-Bottom\nNEST 12-Well Reservoir\nUSA Scientific 12-Well Reservoir, 22mL\nReagents\nSamples\n\n\n\nSlot 1: Opentrons Temperature Module with 96-Well Plate\nSlot 2: 96-Well Plate with Reagents (in lieu of Tube Rack)\nThese should be loaded in the same well number as tube rack\n* A1\n* A2\n* A3\n* A4\n* A5\n* A6\n* B1\n* B2\n* B3\n* B4\n* C1\n* C2\n* C3\n* C4\n* C5\n* C6\n* D1\n* D2\n* D3\n* D4\nSlot 3: NEST 12-Well Reservoir\n* A1: FACS Buffer\n* A3: 'B6' Reagent (for step 5)\n* A12: Empty (for liquid waste)\nSlot 4: Opentrons 20\u00b5L Tips\nSlot 5: Opentrons 20\u00b5L Tips\nSlot 6: Opentrons 300\u00b5L Tips\nSlot 7: Opentrons 20\u00b5L Tips", + "description": "This protocol performs the cell staining protocol as outlined in the 'Cell staining automation' document. This protocol uses a P20 Single (attached to the left mount) and a P300 (attached to the right mount).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Temperature Module\nOpentrons P20 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nOpentrons 300\u00b5L Tips\n96-Well BRANDplates with V-Bottom\nNEST 12-Well Reservoir\nUSA Scientific 12-Well Reservoir, 22mL\nReagents\nSamples\n\n\n\nSlot 1: Opentrons Temperature Module with 96-Well Plate\nSlot 2: 96-Well Plate with Reagents (in lieu of Tube Rack)\nThese should be loaded in the same well number as tube rack\n A1\n A2\n A3\n A4\n A5\n A6\n B1\n B2\n B3\n B4\n C1\n C2\n C3\n C4\n C5\n C6\n D1\n D2\n D3\n D4\nSlot 3: NEST 12-Well Reservoir\n A1: FACS Buffer\n A3: 'B6' Reagent (for step 5)\n* A12: Empty (for liquid waste)\nSlot 4: Opentrons 20\u00b5L Tips\nSlot 5: Opentrons 20\u00b5L Tips\nSlot 6: Opentrons 300\u00b5L Tips\nSlot 7: Opentrons 20\u00b5L Tips", "internal": "13c0b8", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/13ea1e-part2/README.json b/protoBuilds/13ea1e-part2/README.json index 41c66ac60..e1f4d6342 100644 --- a/protoBuilds/13ea1e-part2/README.json +++ b/protoBuilds/13ea1e-part2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck Layout with samples and controls loaded onto 96 well plates.\n\n", - "description": "This protocol preps a 384 well sample plate with mastermix. Up to four plates can be loaded onto the deck with a no template control and human sample control in wells A1 and B1, respectively. Sample plates are transferred to the 384 well plate skipping wells down a column, as well as skipping columns (e.g. plate 1 to A1, C1, E1....H1, A3, C3, E3...etc). A positive control is added to the last well in the 384 well plate.\nThe protocol is broken down into 3 main parts:\n* Mastermix distributed to 384 well plate.\n* Sample added to 384 well plate.\n* Positive control added to plate.\nNote: The protocol will prompt the user to put the specified amount of volume for all 3 mastermix reagents in the specified number of tubes at the beginning of the protocol.\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples (1-96) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n* P20 Single Channel Mount (GEN2): Specify which mount the P20 Single Channel pipette will be mounted.\n* Percent overage: Specify the overage percent to which mastermix will be made and distributed to the 384 well plate.\n* Mix repetitions: Specify the number of mix repetitions for making mastermix, as well as after distributing sample to the mastermix.\n", + "description": "This protocol preps a 384 well sample plate with mastermix. Up to four plates can be loaded onto the deck with a no template control and human sample control in wells A1 and B1, respectively. Sample plates are transferred to the 384 well plate skipping wells down a column, as well as skipping columns (e.g. plate 1 to A1, C1, E1....H1, A3, C3, E3...etc). A positive control is added to the last well in the 384 well plate.\nThe protocol is broken down into 3 main parts:\n Mastermix distributed to 384 well plate.\n Sample added to 384 well plate.\n* Positive control added to plate.\nNote: The protocol will prompt the user to put the specified amount of volume for all 3 mastermix reagents in the specified number of tubes at the beginning of the protocol.\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples (1-96) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n P20 Single Channel Mount (GEN2): Specify which mount the P20 Single Channel pipette will be mounted.\n Percent overage: Specify the overage percent to which mastermix will be made and distributed to the 384 well plate.\n Mix repetitions: Specify the number of mix repetitions for making mastermix, as well as after distributing sample to the mastermix.\n", "internal": "13ea1e-part2", "labware": "\nKingfisher 96 Well Plate\n384 Well Plate\nOpentrons 20\u00b5L Tips\nOpentrons 300\u00b5L Tips\nOpentrons 4-in-1 tube rack with 1.5mL tubes\n", "markdown": { diff --git a/protoBuilds/13ea1e/README.json b/protoBuilds/13ea1e/README.json index 6fda8d6be..022def778 100644 --- a/protoBuilds/13ea1e/README.json +++ b/protoBuilds/13ea1e/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck setup with samples loaded into all wells except A1 and B1.\n\n", - "description": "This protocol preps a sample plate as well as an ethanol, NPW3, NPW4, and elution buffer plate for further use in a Kingfisher Flex Extractor. Samples are pre-loaded onto the sample plate before the protocol begins. Mag beads are then added to sample, and after an incubation step, all other reagent plates are prepped. \nThe protocol is broken down into 3 main parts:\n* Controls are added to sample plate\n* Proteinase K is added to samples\n* Magnetic Beads are added, incubate\n* Sample blocks made\nNote: For all transfers between reservoirs/tubes to well plate, transfers will always iterate over all wells in the source. For example, magnetic beads will be transferred from A1 to plate, A2 to plate, A3 to plate, A4 to plate, A1 to plate, etc. Consequently, all reaction volumes should be split equally into respective wells as seen in the deck layout.\nExplanation of complex parameters below:\n* Number of samples: Specify the number of populated wells (1-96, include controls) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n* Mix repetitions to resuspend beads: Specify the amount of mix steps to re-suspend beads each time the pipette returns to the reservoir.\n* P1000 Single Channel Mount (GEN2): Specify which mount the P1000 Single Channel pipette will be mounted.\n* P300 Multi Channel Mount (GEN2): Specify which mount the P300 Multi Channel pipette will be mounted.\n", + "description": "This protocol preps a sample plate as well as an ethanol, NPW3, NPW4, and elution buffer plate for further use in a Kingfisher Flex Extractor. Samples are pre-loaded onto the sample plate before the protocol begins. Mag beads are then added to sample, and after an incubation step, all other reagent plates are prepped. \nThe protocol is broken down into 3 main parts:\n Controls are added to sample plate\n Proteinase K is added to samples\n Magnetic Beads are added, incubate\n Sample blocks made\nNote: For all transfers between reservoirs/tubes to well plate, transfers will always iterate over all wells in the source. For example, magnetic beads will be transferred from A1 to plate, A2 to plate, A3 to plate, A4 to plate, A1 to plate, etc. Consequently, all reaction volumes should be split equally into respective wells as seen in the deck layout.\nExplanation of complex parameters below:\n Number of samples: Specify the number of populated wells (1-96, include controls) that the sample block, elution buffer block, ethanol block, NPW3 block, and NPW4 block will be filled.\n Mix repetitions to resuspend beads: Specify the amount of mix steps to re-suspend beads each time the pipette returns to the reservoir.\n P1000 Single Channel Mount (GEN2): Specify which mount the P1000 Single Channel pipette will be mounted.\n P300 Multi Channel Mount (GEN2): Specify which mount the P300 Multi Channel pipette will be mounted.\n", "internal": "13ea1e", "labware": "\nKingfisher 96 Well Plate\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 20\u00b5L Tips\nOpentrons 300\u00b5L Tips\nOpentrons 4-in-1 tube rack with 1.5mL tubes\n", "markdown": { diff --git a/protoBuilds/13fd88/README.json b/protoBuilds/13fd88/README.json index 126322e84..4b24819a4 100644 --- a/protoBuilds/13fd88/README.json +++ b/protoBuilds/13fd88/README.json @@ -5,7 +5,7 @@ "Purification" ] }, - "description": "This protocol automates the purification of samples, using magnetic NI resin, ThermoFisher B-PER reagent, and homemade buffers.\n\nThis protocol requires the user to perform some off-deck steps (centrifuge) and replace tips midway. Both actions will be prompted by flashing lights a message in the Opentrons app.\n\nThis protocol uses custom labware definitions for the NEST deep well plate and the Chrom Tech 96-well filter plate. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\n(6) Opentrons 300\u00b5L Tips\nOpentrons Magnetic Module\n(4) NEST 96-Well Plates\nNEST 12-Well Reservoir\nNEST Deep Well Plate\nChrom Tech 96-Well Filter Plate\nSamples\nReagents\n\n\n\nPart 1: B-PER Addition, Incubation, and Transfer\nSlot 10: Opentrons 300\u00b5L Tips\nSlot 11: Opentrons 300\u00b5L Tips\nSlot 8: Opentrons 300\u00b5L Tips\nSlot 9: Opentrons 300\u00b5L Tips\nSlot 7: Opentrons Magnetic Module with NEST 96-Well Plates\nSlot 4: NEST 12-Well Reservoir\n* A1: B-PER Reagent\n* A3: Magnetic NI Resin\n* A5: Wash Buffer (first wash)\n* A7: Wash Buffer (second wash)\n* A9: Elution Buffer\n\nSlot 5: NEST 96-Well Plates\nSlot 1: NEST Deep Well Plate with Samples\n\nThis setup will be sufficient for the protocol up through the addition of the second wash buffer. After the second addition of the wash buffer, the OT-2 will pause and prompt the user to replace the tips in slots 8 and 9, and ensure that the remaining plates are in place (they can be loaded earlier if wanted)\n\nPart 2: 2nd Wash and Elution (in addition to previous labware...)\nSlot 6: NEST 96-Well Plates\nSlot 2: NEST 96-Well Plates\nSlot 3: Chrom Tech 96-Well Filter Plate\n\n", + "description": "This protocol automates the purification of samples, using magnetic NI resin, ThermoFisher B-PER reagent, and homemade buffers.\n\nThis protocol requires the user to perform some off-deck steps (centrifuge) and replace tips midway. Both actions will be prompted by flashing lights a message in the Opentrons app.\n\nThis protocol uses custom labware definitions for the NEST deep well plate and the Chrom Tech 96-well filter plate. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\n(6) Opentrons 300\u00b5L Tips\nOpentrons Magnetic Module\n(4) NEST 96-Well Plates\nNEST 12-Well Reservoir\nNEST Deep Well Plate\nChrom Tech 96-Well Filter Plate\nSamples\nReagents\n\n\n\nPart 1: B-PER Addition, Incubation, and Transfer\nSlot 10: Opentrons 300\u00b5L Tips\nSlot 11: Opentrons 300\u00b5L Tips\nSlot 8: Opentrons 300\u00b5L Tips\nSlot 9: Opentrons 300\u00b5L Tips\nSlot 7: Opentrons Magnetic Module with NEST 96-Well Plates\nSlot 4: NEST 12-Well Reservoir\n A1: B-PER Reagent\n A3: Magnetic NI Resin\n A5: Wash Buffer (first wash)\n A7: Wash Buffer (second wash)\n* A9: Elution Buffer\n\nSlot 5: NEST 96-Well Plates\nSlot 1: NEST Deep Well Plate with Samples\n\nThis setup will be sufficient for the protocol up through the addition of the second wash buffer. After the second addition of the wash buffer, the OT-2 will pause and prompt the user to replace the tips in slots 8 and 9, and ensure that the remaining plates are in place (they can be loaded earlier if wanted)\n\nPart 2: 2nd Wash and Elution (in addition to previous labware...)\nSlot 6: NEST 96-Well Plates\nSlot 2: NEST 96-Well Plates\nSlot 3: Chrom Tech 96-Well Filter Plate\n\n", "internal": "13fd88", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/141a1a/README.json b/protoBuilds/141a1a/README.json index fa1168622..0197695b1 100644 --- a/protoBuilds/141a1a/README.json +++ b/protoBuilds/141a1a/README.json @@ -5,7 +5,7 @@ "Cell-Free Gene Expression" ] }, - "description": "This protocol automates the cell-free gene expression test as outlined by users at TU Munich. See below:\n\nThis protocol sets up a cell-free gene expression experiment (TXTL test) in a 384-well plate. A TXTL sample is composed of cell extract (E), buffer (B), and a plasmid coding for the desired genes. The cell extract and buffer volume in each sample is fixed, the volume of plasmid in each sample depends on the plasmid stock concentration and the desired sample concentration of the plasmid. The final volume of 15\u00b5l is reached by adding nuclease-free water to the sample.\n\nWith the parameters, the user is able to test separate samples for different plasmids coding for the fluorescent proteins (ex. RFP, YFP, GFP and CFP) and measure up to 3 replicates for each of them. In addition, up to two blank samples containing E+B and water are made. First, mastermixes of plasmid and water are made, then distributed to the corresponding wells in the 384-well plate. Then E+B mixes are prepared and also distributed to the corresponding wells.\n\nThis protocol uses a custom labware definition for the Brand 384-well plate. When downloading the protocol, the labware definition (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\nIn the case that the protocol needs more tips than can be accommodated, the robot will pause, flash the rail lights, and ask the user to replace the tiprack.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons Thermocycler Module\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 (GEN2) Single-Channel Pipette\nOpentrons P20 (GEN2) Single-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons 20\u00b5L Tips\n(2) Opentrons 4-in-1 Tube Rack Set, with 24-well top\n1.5mL Centrifuge Tubes\n2mL Centrifuge Tubes\n96-Well Aluminum Block\nPCR Strips\nBrand 384-Well Plate\nReagents\n\n\n\nSlot 1: Brand 384-Well Plate\nSlot 2: Opentrons 4-in-1 Tube Rack Set, with 24-well top with 1.5mL Centrifuge Tubes (for Cell Extracts + Buffer)\nSlot 3: 96-Well Aluminum Block with PCR Strips (containing Buffer aliquots)\nSlot 5: Opentrons 4-in-1 Tube Rack Set, with 24-well top with 2mL Centrifuge Tubes (for Plasmid stock and Nuclease-Free Water)\n* A1: Plasmid 1 Stock (RFP)\n* B1: Plasmid 2 Stock (YFP)\n* C1: Plasmid 3 Stock (GFP)\n* D1: Plasmid 4 Stock (CFP)\n* A3: (Empty) Plasmid 1 Master Mix\n* B3: (Empty) Plasmid 2 Master Mix\n* C3: (Empty) Plasmid 3 Master Mix\n* D3: (Empty) Plasmid 4 Master Mix\n* A5: Nuclease-Free Water\n* D5: (Empty) Pooled Buffer\nSlot 6: Opentrons 20\u00b5L Tips\nSlot 9: Opentrons 300\u00b5L Tips\nSlot 7/8/10/11: Opentrons Thermocycler Module\n\n\nUsing the customizations field (below), set up your protocol.\n* Plasmid Mix CSV: Upload a CSV containing headers (plasmid, molecular weight, concentration, and sample concentration).\n* Number of Replicates (1-3): The number of replicates per plasmid.\n* Number of Cell Extracts (1-24): The number of cell extracts (each extract will be dispensed in a column (1-24)).\n* Number of Blanks per Cell Extract (1, 2): The number of blanks (no plasmid) per cell extract (either 1 or 2).\n* P20 Mount: Select which mount (left or right) the P20 Single is attached to.\n* P300 Mount: Select which mount (left or right) the P300 Single is attached to.", + "description": "This protocol automates the cell-free gene expression test as outlined by users at TU Munich. See below:\n\nThis protocol sets up a cell-free gene expression experiment (TXTL test) in a 384-well plate. A TXTL sample is composed of cell extract (E), buffer (B), and a plasmid coding for the desired genes. The cell extract and buffer volume in each sample is fixed, the volume of plasmid in each sample depends on the plasmid stock concentration and the desired sample concentration of the plasmid. The final volume of 15\u00b5l is reached by adding nuclease-free water to the sample.\n\nWith the parameters, the user is able to test separate samples for different plasmids coding for the fluorescent proteins (ex. RFP, YFP, GFP and CFP) and measure up to 3 replicates for each of them. In addition, up to two blank samples containing E+B and water are made. First, mastermixes of plasmid and water are made, then distributed to the corresponding wells in the 384-well plate. Then E+B mixes are prepared and also distributed to the corresponding wells.\n\nThis protocol uses a custom labware definition for the Brand 384-well plate. When downloading the protocol, the labware definition (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\nIn the case that the protocol needs more tips than can be accommodated, the robot will pause, flash the rail lights, and ask the user to replace the tiprack.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons Thermocycler Module\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 (GEN2) Single-Channel Pipette\nOpentrons P20 (GEN2) Single-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons 20\u00b5L Tips\n(2) Opentrons 4-in-1 Tube Rack Set, with 24-well top\n1.5mL Centrifuge Tubes\n2mL Centrifuge Tubes\n96-Well Aluminum Block\nPCR Strips\nBrand 384-Well Plate\nReagents\n\n\n\nSlot 1: Brand 384-Well Plate\nSlot 2: Opentrons 4-in-1 Tube Rack Set, with 24-well top with 1.5mL Centrifuge Tubes (for Cell Extracts + Buffer)\nSlot 3: 96-Well Aluminum Block with PCR Strips (containing Buffer aliquots)\nSlot 5: Opentrons 4-in-1 Tube Rack Set, with 24-well top with 2mL Centrifuge Tubes (for Plasmid stock and Nuclease-Free Water)\n A1: Plasmid 1 Stock (RFP)\n B1: Plasmid 2 Stock (YFP)\n C1: Plasmid 3 Stock (GFP)\n D1: Plasmid 4 Stock (CFP)\n A3: (Empty) Plasmid 1 Master Mix\n B3: (Empty) Plasmid 2 Master Mix\n C3: (Empty) Plasmid 3 Master Mix\n D3: (Empty) Plasmid 4 Master Mix\n A5: Nuclease-Free Water\n D5: (Empty) Pooled Buffer\nSlot 6: Opentrons 20\u00b5L Tips\nSlot 9: Opentrons 300\u00b5L Tips\nSlot 7/8/10/11: Opentrons Thermocycler Module\n\n\nUsing the customizations field (below), set up your protocol.\n Plasmid Mix CSV: Upload a CSV containing headers (plasmid, molecular weight, concentration, and sample concentration).\n Number of Replicates (1-3): The number of replicates per plasmid.\n Number of Cell Extracts (1-24): The number of cell extracts (each extract will be dispensed in a column (1-24)).\n Number of Blanks per Cell Extract (1, 2): The number of blanks (no plasmid) per cell extract (either 1 or 2).\n P20 Mount: Select which mount (left or right) the P20 Single is attached to.\n P300 Mount: Select which mount (left or right) the P300 Single is attached to.", "internal": "141a1a", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1440ad/README.json b/protoBuilds/1440ad/README.json index 270f3398b..34dff1a60 100644 --- a/protoBuilds/1440ad/README.json +++ b/protoBuilds/1440ad/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol extracts RNA using two temperature modules and a magnetic module. The protocol can be considered in 5 main parts:\n\nReagent added to sample\nSample moved to magnetic plate\nMag Beads added to sample\nTwo ethanol washes with magnet engagement\nWater added to samples\nSamples added to final tube rack\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples for this run.\n* Number of Mag Bead Tubes: Specify the number of tubes to store the magnetic beads in column 6 of the room temperature reagent rack. Note: mag bead volume should be split equally between the number of tubes specified. \n* Mag Bead Resuspend Volume: Specify the volume to mix the beads for resuspension before they are added to a sample.\n* Mag Bead Resuspend Mix Repetions: Specify the number of repetitions to mix Mag Bead Resuspend Volume before the mag beads are added to the sample.\n* RR1-TR10 Volume: Specify the volume of each respective reagent to put into each sample.\n* P20 Single Channel Mount: Specify which mount (left or right) to place the P20 single channel pipette.\n* P300 Single Channel Mount: Specify which mount (left or right) to place the P20 single channel pipette.\n", + "description": "This protocol extracts RNA using two temperature modules and a magnetic module. The protocol can be considered in 5 main parts:\n\nReagent added to sample\nSample moved to magnetic plate\nMag Beads added to sample\nTwo ethanol washes with magnet engagement\nWater added to samples\nSamples added to final tube rack\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples for this run.\n Number of Mag Bead Tubes: Specify the number of tubes to store the magnetic beads in column 6 of the room temperature reagent rack. Note: mag bead volume should be split equally between the number of tubes specified. \n Mag Bead Resuspend Volume: Specify the volume to mix the beads for resuspension before they are added to a sample.\n Mag Bead Resuspend Mix Repetions: Specify the number of repetitions to mix Mag Bead Resuspend Volume before the mag beads are added to the sample.\n RR1-TR10 Volume: Specify the volume of each respective reagent to put into each sample.\n P20 Single Channel Mount: Specify which mount (left or right) to place the P20 single channel pipette.\n* P300 Single Channel Mount: Specify which mount (left or right) to place the P20 single channel pipette.\n", "internal": "1440ad", "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\n4-in-1 Tube Rack Set\nOpentrons 300uL Tips\nOpentrons 20\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/1464-2/README.json b/protoBuilds/1464-2/README.json index 9d6366320..40dcc6f20 100644 --- a/protoBuilds/1464-2/README.json +++ b/protoBuilds/1464-2/README.json @@ -5,7 +5,7 @@ "ELISA" ] }, - "description": "Links:\n* Part 1: Dilution\n* Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addition\nThis is the second part of a ELISA protocol: Antibody Addition. The robot will first add Enzyme Conjugate Reagent to all of the columns required in the output plate in slot 9. Water, diluent, and HCP standards, and diluted samples will be transferred to the output plate in duplicate. User will need to upload the same CSV file used in part 1 of the protocol. See Additional Notes in Part 1 for more details on the CSV requirements.\nDownload full protocol details here.\n\nYou will need:\n* P300 Multi-channel Pipette\n* P300 Single-channel Pipette\n* Opentrons Tube Racks (2 mL Eppendorf)\n* Opentrons Tube Rack (15 + 50 mL)\n* 2 mL 96-deep well Plate\n* 96-well Plate\n* 12-row Trough\n* 300 uL Tip Racks", + "description": "Links:\n Part 1: Dilution\n Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addition\nThis is the second part of a ELISA protocol: Antibody Addition. The robot will first add Enzyme Conjugate Reagent to all of the columns required in the output plate in slot 9. Water, diluent, and HCP standards, and diluted samples will be transferred to the output plate in duplicate. User will need to upload the same CSV file used in part 1 of the protocol. See Additional Notes in Part 1 for more details on the CSV requirements.\nDownload full protocol details here.\n\nYou will need:\n P300 Multi-channel Pipette\n P300 Single-channel Pipette\n Opentrons Tube Racks (2 mL Eppendorf)\n Opentrons Tube Rack (15 + 50 mL)\n 2 mL 96-deep well Plate\n 96-well Plate\n 12-row Trough\n 300 uL Tip Racks", "internal": "AwOUI09G\n1464", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", @@ -17,7 +17,7 @@ "robot": "* [OT-2](https://opentrons.com/ot-2)\n\n", "title": "ELISA Protocol 2/3: Antibody Addition" }, - "notes": "Tube Rack setup: (slot 4)\n* DI Water: A1\n* Diluent: A2\n* HCP Standards: A3-B2 if number of standards is 6, A3-B4 if 8\n* Samples: B3-(D6) if number of standards is 6, B5-(D6) if 8\nYou will need to shift the locations of the samples based on the number of standards you have each run. This configuration must be consistent of that of part 1.\n\nIf you have any questions about this protocol, please contact protocols@opentrons.com.", + "notes": "Tube Rack setup: (slot 4)\n DI Water: A1\n Diluent: A2\n HCP Standards: A3-B2 if number of standards is 6, A3-B4 if 8\n Samples: B3-(D6) if number of standards is 6, B5-(D6) if 8\nYou will need to shift the locations of the samples based on the number of standards you have each run. This configuration must be consistent of that of part 1.\n\nIf you have any questions about this protocol, please contact protocols@opentrons.com.", "process": "\nSelect the number of standards you are using.\nUpload the same concentration CSV you uploaded to part 1 of the protocol.\nDownload your protocol.\nUpload your protocol into the OT App.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support article.\nHit \"Run\".\n", "robot": [ "OT-2" diff --git a/protoBuilds/1464-3/README.json b/protoBuilds/1464-3/README.json index bbe56c2fe..771a321a0 100644 --- a/protoBuilds/1464-3/README.json +++ b/protoBuilds/1464-3/README.json @@ -5,7 +5,7 @@ "ELISA" ] }, - "description": "Links:\n* Part 1: Dilution\n* Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addtion\nThis is the third part of a ELISA protocol: Substrate and Stop Solution Addition. This should be run immediately after the incubation and wash steps.\nDownload full protocol details here.\n\nYou will need:\n* P300 Multi-channel Pipette\n* P300 Single-channel Pipette\n* Opentrons Tube Racks (2 mL Eppendorf)\n* Opentrons Tube Rack (15 + 50 mL)\n* 96-well Plate\n* 12-row Trough\n* 300 uL Tip Racks", + "description": "Links:\n Part 1: Dilution\n Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addtion\nThis is the third part of a ELISA protocol: Substrate and Stop Solution Addition. This should be run immediately after the incubation and wash steps.\nDownload full protocol details here.\n\nYou will need:\n P300 Multi-channel Pipette\n P300 Single-channel Pipette\n Opentrons Tube Racks (2 mL Eppendorf)\n Opentrons Tube Rack (15 + 50 mL)\n 96-well Plate\n 12-row Trough\n* 300 uL Tip Racks", "internal": "AwOUI09G\n1464", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", diff --git a/protoBuilds/1464/README.json b/protoBuilds/1464/README.json index 7791c0aeb..a4e0da7e7 100644 --- a/protoBuilds/1464/README.json +++ b/protoBuilds/1464/README.json @@ -5,7 +5,7 @@ "ELISA" ] }, - "description": "Links:\n* Part 1: Dilution\n* Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addition\nThis is the first part of a ELISA protocol: Dilution Procedure. The robot will perform serial dilutions samples located in the Opentrons 2 mL Eppendorf tube rack in the 1.2 mL tube plates. User will need to upload a CSV specifying the desired concentrations of each sample to be transferred to a separate 96-well plate in part 2 of the protocol. See more information on the CSV requirement in Additional Notes below.\nDownload full protocol details here.\n\nYou will need:\n* P1000 Single-channel Pipette\n* P300 Single-channel Pipette\n* Opentrons Tube Racks (2 mL Eppendorf)\n* Opentrons Tube Rack (15 + 50 mL)\n* 2 mL 96-deep well Plate\n* 96-well Plate\n* 12-row Trough\n* 1000 uL Tip Rack\n* 300 uL Tip Rack", + "description": "Links:\n Part 1: Dilution\n Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addition\nThis is the first part of a ELISA protocol: Dilution Procedure. The robot will perform serial dilutions samples located in the Opentrons 2 mL Eppendorf tube rack in the 1.2 mL tube plates. User will need to upload a CSV specifying the desired concentrations of each sample to be transferred to a separate 96-well plate in part 2 of the protocol. See more information on the CSV requirement in Additional Notes below.\nDownload full protocol details here.\n\nYou will need:\n P1000 Single-channel Pipette\n P300 Single-channel Pipette\n Opentrons Tube Racks (2 mL Eppendorf)\n Opentrons Tube Rack (15 + 50 mL)\n 2 mL 96-deep well Plate\n 96-well Plate\n 12-row Trough\n 1000 uL Tip Rack\n* 300 uL Tip Rack", "internal": "1464", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", @@ -17,7 +17,7 @@ "robot": "* [OT-2](https://opentrons.com/ot-2)\n\n", "title": "ELISA Protocol 1/3: Dilution" }, - "notes": "Tube Rack setup: (slot 4)\n* DI Water: A1\n* Diluent: A2\n* HCP Standards: A3-B2 if number of standards is 6, A3-B4 if 8\n* Samples: B3-(D6) if number of standards is 6, B5-(D6) if 8\nYou will need to shift the locations of the samples based on the number of standards you have each run. This configuration must be consistent of that of part 2.\n\nCSV Layout:\n\n\nNo headers\nEach row represents each sample\nEach column represents the dilution factor of that sample to be transferred to the output plate in part 2 of the protocol\nRobot will determine the dilution scheme of each sample based on the concentrations in the CSV\n\n\nIf you have any questions about this protocol, please contact protocols@opentrons.com.", + "notes": "Tube Rack setup: (slot 4)\n DI Water: A1\n Diluent: A2\n HCP Standards: A3-B2 if number of standards is 6, A3-B4 if 8\n Samples: B3-(D6) if number of standards is 6, B5-(D6) if 8\nYou will need to shift the locations of the samples based on the number of standards you have each run. This configuration must be consistent of that of part 2.\n\nCSV Layout:\n\n\nNo headers\nEach row represents each sample\nEach column represents the dilution factor of that sample to be transferred to the output plate in part 2 of the protocol\nRobot will determine the dilution scheme of each sample based on the concentrations in the CSV\n\n\nIf you have any questions about this protocol, please contact protocols@opentrons.com.", "process": "\nDownload your protocol.\nUpload your protocol into the OT App.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support article.\nHit \"Run\".\n", "robot": [ "OT-2" diff --git a/protoBuilds/1477ea/README.json b/protoBuilds/1477ea/README.json index d537cf8df..a0c0e2d69 100644 --- a/protoBuilds/1477ea/README.json +++ b/protoBuilds/1477ea/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nOpentrons p300 tips (Deck Slots 10, 11)\nOpentrons p20 tips (Deck Slot 7)\n195 mL NEST 1 Well Reservoir (Deck Slot 4)\nSource Plate (TPP 96 well tissue culture plate Deck Slot 8)\nDestination Plate (NUNC WHITE 96F 236105 96 well plate Deck Slot 6)\n", - "description": "This protocol cherrypicks from source plate wells specified in the first column of an input CSV file and transfers 2 ul of the well's contents to destination plate wells specified in the second column of the input CSV file.\nLinks:\n* Custom Cherrypicking json Protocol\n* Opentrons Protocol Designer No-Code Tool\n* Sample CSV File\nThis protocol is a python translation of the attached custom cherrypicking json protocol that can be downloaded from the link above (and then uploaded to the online Opentrons Protocol Designer tool). This python translation has an added feature: upload of an input CSV file to specify source and destination wells.", + "description": "This protocol cherrypicks from source plate wells specified in the first column of an input CSV file and transfers 2 ul of the well's contents to destination plate wells specified in the second column of the input CSV file.\nLinks:\n Custom Cherrypicking json Protocol\n Opentrons Protocol Designer No-Code Tool\n* Sample CSV File\nThis protocol is a python translation of the attached custom cherrypicking json protocol that can be downloaded from the link above (and then uploaded to the online Opentrons Protocol Designer tool). This python translation has an added feature: upload of an input CSV file to specify source and destination wells.", "internal": "1477ea", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1577-v2/README.json b/protoBuilds/1577-v2/README.json index 20a0644b3..4337a3e19 100644 --- a/protoBuilds/1577-v2/README.json +++ b/protoBuilds/1577-v2/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol performs PCR preparation on a custom 3x8 membrane chip on 6 PCR strips. Ensure that the chip is seated so that the wells of the second (middle) row are slightly offset to the top of the first and third rows as shown in 'Additional Notes' below. Please calibrate the custom chip so that the pipette tip lands lands just barely above the membrane-- this will ensure accurate liquid transfer without disturbing the eggs or crashing into the chip. For reagent setup, see 'Additional Notes' below.\n\n\n\nP10 Multi-channel electronic pipette\n10\u00b5l Pipette tips\nP50 Single-channel electronic pipette\n300\u00b5l Pipette tips\nOpentrons 4-in-1 tube rack set\nTempassure 200ml PCR strips (seated)\n1.7ml Eppendorf tubes\nCustom 3x8 offset membrane chip on shaker (mounted on OT-2 deck)\n\n\n\n4x6 tuberack for 2ml Eppendorf tubes:\n* tube A1: nanopure H2O\n* tube B1: reaction buffer\n* tube C1: primer\n* tube D1: DNA polymerase\n* tube A2: mastermix tube (loaded empty)\nSeated PCR strips:\n* strip column 12: nanopure H2O (for additions with P10-multi channel pipette)", + "description": "This protocol performs PCR preparation on a custom 3x8 membrane chip on 6 PCR strips. Ensure that the chip is seated so that the wells of the second (middle) row are slightly offset to the top of the first and third rows as shown in 'Additional Notes' below. Please calibrate the custom chip so that the pipette tip lands lands just barely above the membrane-- this will ensure accurate liquid transfer without disturbing the eggs or crashing into the chip. For reagent setup, see 'Additional Notes' below.\n\n\n\nP10 Multi-channel electronic pipette\n10\u00b5l Pipette tips\nP50 Single-channel electronic pipette\n300\u00b5l Pipette tips\nOpentrons 4-in-1 tube rack set\nTempassure 200ml PCR strips (seated)\n1.7ml Eppendorf tubes\nCustom 3x8 offset membrane chip on shaker (mounted on OT-2 deck)\n\n\n\n4x6 tuberack for 2ml Eppendorf tubes:\n tube A1: nanopure H2O\n tube B1: reaction buffer\n tube C1: primer\n tube D1: DNA polymerase\n* tube A2: mastermix tube (loaded empty)\nSeated PCR strips:\n* strip column 12: nanopure H2O (for additions with P10-multi channel pipette)", "internal": "yYlOorFh\n1577", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", diff --git a/protoBuilds/158d42/README.json b/protoBuilds/158d42/README.json index 740036ec6..fb9e997d6 100644 --- a/protoBuilds/158d42/README.json +++ b/protoBuilds/158d42/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n24 tube racks should be placed in order of slots 9, 6. Tubes by row.\n32 tube racks should be placed in order of slots 7 and 4. Tubes by row.\n\n\n", - "description": "This protocol preps a 96 well PCR plate with up to 46 samples. The order of operations is: transfer negative control to A1 of the well plate, transfer samples down plate columns starting from C1, transfer positive control to A12 of well plate, then B1. Resuspension steps are included after most transfers. For wells with powdered reagent, roughly half of the necessary volume is dispensed into the well from half of the well depth, then the pipette tip proceeds to travel to the bottom of the well to dispense the rest of the required volume and mix. Sample in buffer is transferred from the 32-tube rack to the 24 tube rack which contains sterile normalization buffer, and the resulting mixture is then added to the plate.\nExplanation of complex parameters below:\n* Number of tubes (1-46): Specify the number of tubes placed in the custom 32-tube tube racks. Tubes should be placed by row, and up down (from slot 7 to slot 4).\n* Use Temperature Module: Specify whether or not to use the temperature module at 12C this run. If not, you can place the plate directly on slot 1.\n* P300 Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n", + "description": "This protocol preps a 96 well PCR plate with up to 46 samples. The order of operations is: transfer negative control to A1 of the well plate, transfer samples down plate columns starting from C1, transfer positive control to A12 of well plate, then B1. Resuspension steps are included after most transfers. For wells with powdered reagent, roughly half of the necessary volume is dispensed into the well from half of the well depth, then the pipette tip proceeds to travel to the bottom of the well to dispense the rest of the required volume and mix. Sample in buffer is transferred from the 32-tube rack to the 24 tube rack which contains sterile normalization buffer, and the resulting mixture is then added to the plate.\nExplanation of complex parameters below:\n Number of tubes (1-46): Specify the number of tubes placed in the custom 32-tube tube racks. Tubes should be placed by row, and up down (from slot 7 to slot 4).\n Use Temperature Module: Specify whether or not to use the temperature module at 12C this run. If not, you can place the plate directly on slot 1.\n* P300 Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n", "internal": "1584d2", "labware": "\nOpentrons 4-in-1 24 tube tube rack with 1.5mL tubes\nNEST 100ul PCR Plate, Full Skirt\nOpentrons 200ul Filter tips\nCustom 32 tube tube racklink to labware on shop.opentrons.com when applicable\n", "markdown": { diff --git a/protoBuilds/1601a9/README.json b/protoBuilds/1601a9/README.json index f74c4c577..d7f507798 100644 --- a/protoBuilds/1601a9/README.json +++ b/protoBuilds/1601a9/README.json @@ -5,7 +5,7 @@ "Illumina Beachip Amplification" ] }, - "description": "This protocol automates sample distribution and the addition of MA1 and 0.1 N NaOH.\nUsing the customizations fields, below set up your protocol.\n* P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Multi-Channel Pipette\nOpentrons 10\u00b5L Tips\nNEST 12-Well Reservoir, 15mL\nAxygen 96-Well Plate (PCR-96-FS-C)\nAbgene 96-Deep Well Plate (AB0765)\nReagents\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n* A5: MA1\n* A9: 0.1 N NaOH\nSlot 2: Abgene 96-Deep Well Plate (AB0765)\nSlot 3: Axygen 96-Well Plate (PCR-96-FS-C)\nSlot 4: Opentrons 10\u00b5L Tips\nSlot 5: Opentrons 10\u00b5L Tips", + "description": "This protocol automates sample distribution and the addition of MA1 and 0.1 N NaOH.\nUsing the customizations fields, below set up your protocol.\n* P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Multi-Channel Pipette\nOpentrons 10\u00b5L Tips\nNEST 12-Well Reservoir, 15mL\nAxygen 96-Well Plate (PCR-96-FS-C)\nAbgene 96-Deep Well Plate (AB0765)\nReagents\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n A5: MA1\n A9: 0.1 N NaOH\nSlot 2: Abgene 96-Deep Well Plate (AB0765)\nSlot 3: Axygen 96-Well Plate (PCR-96-FS-C)\nSlot 4: Opentrons 10\u00b5L Tips\nSlot 5: Opentrons 10\u00b5L Tips", "internal": "1601a9", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/17cb2d/README.json b/protoBuilds/17cb2d/README.json index cf4980234..b4a6cc753 100644 --- a/protoBuilds/17cb2d/README.json +++ b/protoBuilds/17cb2d/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol fills Applied Biosystems MicroAmp 384-well plates with mastermix. Update: this protocol can now accomodate the SSI 384-well plate as well.\n\nThe protocol can fill up to 9 plates and will dispense 7.5\u00b5L of mastermix 1 into all the odd rows (A/C/E...) and 7.5\u00b5L of mastermix 2 into all the even rows (B/D/F...).\n\nThis protocol has been updated to use the GEN2 Multi-Channel Pipettes - please use corresponding tips.\n\nUpdate 09-21-20: The protocol will now do a blow out in the well and aspirate 2\u00b5L of air at the top of the well after each dispense step to ensure all liquid has been expelled from pipette and minimize contamination risk due to droplet hang.\n\nUpdate 09-25-20: The protocol has been updated in two ways. First, the mastermix should be split between two wells (A1/A2 and A11/A12). Second, after aspirating the mastermix, the pipette will move to the sides of the well to remove liquid attached to the tips.\n\nUpdate 10-29-20: The protocol will now transfer 10\u00b5L of mastermix.\n\nUpdate 10-30-20: The protocol will now multi-dispense mastermix instead of 1-to-1 transfer. \n\nUpdate 11-12-20: The protocol now has a new parameter for master mix volume (default is 7.5\u00b5L)\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Multi-Channel Pipette\nOpentrons Tips\nNEST 12-Well Reservoir\nApplied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate\nReagents (mastermix 1, mastermix 2)\n\n\n\nSlots 1 - 9: Applied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate\nSlot 10: Opentrons Tips\nSlot 11: NEST 12-Well Reservoir\nA1: Mastermix 1 (for plates 1-5)\nA2: Mastermix 1 (for plates 6-9)\nA11: Mastermix 2 (for plates 1-5)\nA12: Mastermix 2 (for plates 6-9)\n\n\nUsing the customizations field (below), set up your protocol.\n* Pipette Type: Select which GEN2 Multi-Channel Pipette (p300 or p20) will be used\n* Pipette Mount: Select which mount (left or right) the Multi-Channel Pipette is attached to\n* Number of Plates (1-9): Specify the number of plates to fill\n* Plate (384-Well) Type: Select which plate (Applied Biosystems or SSI) to use\n* Master Mix Volume (uL): Input the volume of master mix to be transferred to each well", + "description": "This protocol fills Applied Biosystems MicroAmp 384-well plates with mastermix. Update: this protocol can now accomodate the SSI 384-well plate as well.\n\nThe protocol can fill up to 9 plates and will dispense 7.5\u00b5L of mastermix 1 into all the odd rows (A/C/E...) and 7.5\u00b5L of mastermix 2 into all the even rows (B/D/F...).\n\nThis protocol has been updated to use the GEN2 Multi-Channel Pipettes - please use corresponding tips.\n\nUpdate 09-21-20: The protocol will now do a blow out in the well and aspirate 2\u00b5L of air at the top of the well after each dispense step to ensure all liquid has been expelled from pipette and minimize contamination risk due to droplet hang.\n\nUpdate 09-25-20: The protocol has been updated in two ways. First, the mastermix should be split between two wells (A1/A2 and A11/A12). Second, after aspirating the mastermix, the pipette will move to the sides of the well to remove liquid attached to the tips.\n\nUpdate 10-29-20: The protocol will now transfer 10\u00b5L of mastermix.\n\nUpdate 10-30-20: The protocol will now multi-dispense mastermix instead of 1-to-1 transfer. \n\nUpdate 11-12-20: The protocol now has a new parameter for master mix volume (default is 7.5\u00b5L)\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Multi-Channel Pipette\nOpentrons Tips\nNEST 12-Well Reservoir\nApplied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate\nReagents (mastermix 1, mastermix 2)\n\n\n\nSlots 1 - 9: Applied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate\nSlot 10: Opentrons Tips\nSlot 11: NEST 12-Well Reservoir\nA1: Mastermix 1 (for plates 1-5)\nA2: Mastermix 1 (for plates 6-9)\nA11: Mastermix 2 (for plates 1-5)\nA12: Mastermix 2 (for plates 6-9)\n\n\nUsing the customizations field (below), set up your protocol.\n Pipette Type: Select which GEN2 Multi-Channel Pipette (p300 or p20) will be used\n Pipette Mount: Select which mount (left or right) the Multi-Channel Pipette is attached to\n Number of Plates (1-9): Specify the number of plates to fill\n Plate (384-Well) Type: Select which plate (Applied Biosystems or SSI) to use\n* Master Mix Volume (uL): Input the volume of master mix to be transferred to each well", "internal": "17cb2d", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/17d210-part-2/README.json b/protoBuilds/17d210-part-2/README.json index 564b111d9..762eb9df5 100644 --- a/protoBuilds/17d210-part-2/README.json +++ b/protoBuilds/17d210-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nblue: PCR2 buffer \npink: samples \ngreen: indexes\n\n\n", - "description": "Links:\n* Part 1\n\n* Part 2\n\n* Part 3\n\n* Part 4\n\n* Part 5\nThis custom indexing protocol is part 2/5 of the Verogen ForenSeq DNA Signature Prep kit. In this protocol, indexes are transferred to their corresponding wells in a PCR plate containing samples. Then, PCR2 buffer is added to each sample and mixed using fresh tips for each transfer.\n", + "description": "Links:\n Part 1\n\n Part 2\n\n Part 3\n\n Part 4\n\n* Part 5\nThis custom indexing protocol is part 2/5 of the Verogen ForenSeq DNA Signature Prep kit. In this protocol, indexes are transferred to their corresponding wells in a PCR plate containing samples. Then, PCR2 buffer is added to each sample and mixed using fresh tips for each transfer.\n", "internal": "17d210", "labware": "\nAbgene Midi 96 Well Plate 800 \u00b5L\nAmplifyt 96 Well Plate 200 \u00b5L\nOpentrons 20\u00b5l and 300\u00b5l Tipracks\n", "markdown": { diff --git a/protoBuilds/17d210-part-3/README.json b/protoBuilds/17d210-part-3/README.json index 6d4cf8d42..52f30c0a7 100644 --- a/protoBuilds/17d210-part-3/README.json +++ b/protoBuilds/17d210-part-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\ngreen: samples\nblue: binding bead buffer\npink: 80% EtOH \npurple: elution buffer\n\n\n", - "description": "Links:\n* Part 1\n\n* Part 2\n\n* Part 3\n\n* Part 4\n\n* Part 5\nThis custom Library Purification protocol is part 3/5 of the Verogen ForenSeq DNA Signature Prep kit. The protocol is broken down into 4 main parts:\n* binding buffer addition to samples\n* bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", + "description": "Links:\n Part 1\n\n Part 2\n\n Part 3\n\n Part 4\n\n* Part 5\nThis custom Library Purification protocol is part 3/5 of the Verogen ForenSeq DNA Signature Prep kit. The protocol is broken down into 4 main parts:\n binding buffer addition to samples\n bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", "internal": "17d210", "labware": "\nAbgene Midi 96 Well Plate 800 \u00b5L\nAmplifyt 96 Well Plate 200 \u00b5L\nNEST 12 Well Reservoir 15 mL\nOpentrons 20\u00b5l and 300\u00b5l Tipracks\n", "markdown": { diff --git a/protoBuilds/17d210-part-4/README.json b/protoBuilds/17d210-part-4/README.json index ed6bb92c2..26b3a1026 100644 --- a/protoBuilds/17d210-part-4/README.json +++ b/protoBuilds/17d210-part-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\ngreen: samples\nblue: binding bead buffer\npink: wash solution \npurple: HP3 dilution\norange: LNS2\n\n\n", - "description": "Links:\n* Part 1\n\n* Part 2\n\n* Part 3\n\n* Part 4\n\n* Part 5\nThis custom extraction protocol is part 4/5 of the Verogen ForenSeq DNA Signature Prep kit. The protocol is broken down into 4 main parts:\n* binding buffer addition to samples\n* bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", + "description": "Links:\n Part 1\n\n Part 2\n\n Part 3\n\n Part 4\n\n* Part 5\nThis custom extraction protocol is part 4/5 of the Verogen ForenSeq DNA Signature Prep kit. The protocol is broken down into 4 main parts:\n binding buffer addition to samples\n bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", "internal": "17d210", "labware": "\nAbgene Midi 96 Well Plate 800 \u00b5L\nAmplifyt 96 Well Plate 200 \u00b5L\nNEST 12 Well Reservoir 15 mL\nOpentrons 20\u00b5l and 300\u00b5l Tipracks\n", "markdown": { diff --git a/protoBuilds/17d210-part-5/README.json b/protoBuilds/17d210-part-5/README.json index 31f9d11e2..a9aec1cda 100644 --- a/protoBuilds/17d210-part-5/README.json +++ b/protoBuilds/17d210-part-5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nblue: pooling strip \ngreen: samples\n\n\n", - "description": "Links:\n* Part 1\n\n* Part 2\n\n* Part 3\n\n* Part 4\n\n* Part 5\nThis custom pooling protocol is part 5/5 of the Verogen ForenSeq DNA Signature Prep kit. In this protocol, samples are pooled from a PCR plate to a final pooling strip.\n", + "description": "Links:\n Part 1\n\n Part 2\n\n Part 3\n\n Part 4\n\n* Part 5\nThis custom pooling protocol is part 5/5 of the Verogen ForenSeq DNA Signature Prep kit. In this protocol, samples are pooled from a PCR plate to a final pooling strip.\n", "internal": "17d210", "labware": "\nAmplifyt 96 Well Plate 200 \u00b5L\nOpentrons 20\u00b5l Tiprack\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/17d210/README.json b/protoBuilds/17d210/README.json index 60d0c7d07..38e0a5e96 100644 --- a/protoBuilds/17d210/README.json +++ b/protoBuilds/17d210/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Part 1\n\n* Part 2\n\n* Part 3\n\n* Part 4\n\n* Part 5\nThis custom PCR1 Setup protocol is part 1/5 of the Verogen ForenSeq DNA Signature Prep kit. In this protocol, mastermix is pre-added to a clean PCR plate. Then, samples from up to 4 source plates specified in the .csv file are transferred to the plate containing mastermix and mixed (optionally).\nThe .csv file should be formatted as shown below (including header line):\nvolume,source plate # (1-4),source column (1-12),destination column(1-12)\n8,1,2,1\n8,2,3,2\n8,2,12,3\n", + "description": "Links:\n Part 1\n\n Part 2\n\n Part 3\n\n Part 4\n\n* Part 5\nThis custom PCR1 Setup protocol is part 1/5 of the Verogen ForenSeq DNA Signature Prep kit. In this protocol, mastermix is pre-added to a clean PCR plate. Then, samples from up to 4 source plates specified in the .csv file are transferred to the plate containing mastermix and mixed (optionally).\nThe .csv file should be formatted as shown below (including header line):\nvolume,source plate # (1-4),source column (1-12),destination column(1-12)\n8,1,2,1\n8,2,3,2\n8,2,12,3\n", "internal": "17d210", "labware": "\nAmplifyt 96 Well Plate 200 \u00b5L\nOpentrons 20\u00b5l Tipracks\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/18d6a1/README.json b/protoBuilds/18d6a1/README.json index 238c50729..d8e35f011 100644 --- a/protoBuilds/18d6a1/README.json +++ b/protoBuilds/18d6a1/README.json @@ -5,7 +5,7 @@ "Nucleic Acid Extraction" ] }, - "description": "This protocol automates the MGI Easy Nucleic Acid Extraction Kit and offers the user the ability to modify parameters such as the number of samples and the types of labware used.\n\nThis protocol has been optimized for use on the OT-2 and begins with an empty deepwell plate on the Magnetic Module. Lysis mix is first added to the plate, then samples are transferred to the lysis mix and mixed. Three wash steps occur after this and the protocol concludes with an elution step that results in 75\u00b5L of elutes transferred to a clean plate.\n\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons Magnetic Module, GEN2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tip Racks for P300\nNEST 1-Well Reservoir, 195mL\nNEST 12-Well Reservoir, 15mL\n96-Well Plate Containing Samples (such as the NEST 96-Well Deep Well Plate)\n96-Deepwell Plate for Extraction on the Magnetic Module (such as the NEST 96-Well Deep Well Plate)\n96-Well Plate for Elutes (such as the NEST 96-Well PCR Plate)\nMGI Easy Nucleic Acid Extraction Kit\n\n\n\nDeck Layout\n\nSlot 1: 96-Well Plate for Elutes (such as the NEST 96-Well PCR Plate)\n\n\nSlot 2: Opentrons Tip Racks for P300 - Tip rack 5\n\n\nSlot 3: NEST 12-Well Reservoir, 15mL\nA1: Lysis Mix (Samples 1-32)\n\nA2: Lysis Mix (Samples 33-64)\n\nA3: Lysis Mix (Samples 65-96)\n\nA4: Wash Buffer 1 (Samples 1-48)\n\nA5: Wash Buffer 1 (Samples 49-96)\n\nA6: Wash Buffer 2 (Samples 1-48)\n\nA7: Wash Buffer 2 (Samples 49-96)\n\nA8: Wash Buffer 3 (Samples 1-48)\n\nA9: Wash Buffer 3 (Samples 49-96)\n\nA10: Empty\n\nA11: Empty\n\nA12: Nuclease-Free Water (Samples 1-96)\n\n\nSlot 4: 96-Well Plate Containing Samples (such as the NEST 96-Well Deep Well Plate)\n\n\nSlot 5: Opentrons Tip Racks for P300 - Tip rack 3\n\n\nSlot 6: Opentrons Tip Racks for P300 - Tip rack 4\n\n\nSlot 7: Opentrons Tip Racks for P300 - Tip rack for Samples\n\n\nSlot 8: Opentrons Tip Racks for P300 - Tip rack 1\n\n\nSlot 9: Opentrons Tip Racks for P300 - Tip rack 2\n\n\nSlot 10: Opentrons Magnetic Module, GEN2 with 96-Deepwell Plate for Extraction (such as the NEST 96-Well Deep Well Plate)\n\n\nSlot 11: NEST 1-Well Reservoir, 195mL (liquid waste)\n\n\nNote about Tip Racks: Each column of samples (8) will require five columns of tips + the tips needed for the initial sample transfer. \n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify the number of samples to run.\n* Sample Plate (input) Type: Select the type of plate used.\n* Extraction Plate (MagPlate) Type: Select the type of plate used.\n* Elution Plate (output) Type: Select the type of plate used.\n* P300-Multi Mount: Select which mount (left, right) the P300-Multi is attached to.\n* Tip Type: Specify the type of tips (filtered, non-filtered) used.\n* Used Tips Destination: Specify the destination of used tips. \"Empty Tipracks\" is best suited for runs of more than 24 samples.", + "description": "This protocol automates the MGI Easy Nucleic Acid Extraction Kit and offers the user the ability to modify parameters such as the number of samples and the types of labware used.\n\nThis protocol has been optimized for use on the OT-2 and begins with an empty deepwell plate on the Magnetic Module. Lysis mix is first added to the plate, then samples are transferred to the lysis mix and mixed. Three wash steps occur after this and the protocol concludes with an elution step that results in 75\u00b5L of elutes transferred to a clean plate.\n\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons Magnetic Module, GEN2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tip Racks for P300\nNEST 1-Well Reservoir, 195mL\nNEST 12-Well Reservoir, 15mL\n96-Well Plate Containing Samples (such as the NEST 96-Well Deep Well Plate)\n96-Deepwell Plate for Extraction on the Magnetic Module (such as the NEST 96-Well Deep Well Plate)\n96-Well Plate for Elutes (such as the NEST 96-Well PCR Plate)\nMGI Easy Nucleic Acid Extraction Kit\n\n\n\nDeck Layout\n\nSlot 1: 96-Well Plate for Elutes (such as the NEST 96-Well PCR Plate)\n\n\nSlot 2: Opentrons Tip Racks for P300 - Tip rack 5\n\n\nSlot 3: NEST 12-Well Reservoir, 15mL\nA1: Lysis Mix (Samples 1-32)\n\nA2: Lysis Mix (Samples 33-64)\n\nA3: Lysis Mix (Samples 65-96)\n\nA4: Wash Buffer 1 (Samples 1-48)\n\nA5: Wash Buffer 1 (Samples 49-96)\n\nA6: Wash Buffer 2 (Samples 1-48)\n\nA7: Wash Buffer 2 (Samples 49-96)\n\nA8: Wash Buffer 3 (Samples 1-48)\n\nA9: Wash Buffer 3 (Samples 49-96)\n\nA10: Empty\n\nA11: Empty\n\nA12: Nuclease-Free Water (Samples 1-96)\n\n\nSlot 4: 96-Well Plate Containing Samples (such as the NEST 96-Well Deep Well Plate)\n\n\nSlot 5: Opentrons Tip Racks for P300 - Tip rack 3\n\n\nSlot 6: Opentrons Tip Racks for P300 - Tip rack 4\n\n\nSlot 7: Opentrons Tip Racks for P300 - Tip rack for Samples\n\n\nSlot 8: Opentrons Tip Racks for P300 - Tip rack 1\n\n\nSlot 9: Opentrons Tip Racks for P300 - Tip rack 2\n\n\nSlot 10: Opentrons Magnetic Module, GEN2 with 96-Deepwell Plate for Extraction (such as the NEST 96-Well Deep Well Plate)\n\n\nSlot 11: NEST 1-Well Reservoir, 195mL (liquid waste)\n\n\nNote about Tip Racks: Each column of samples (8) will require five columns of tips + the tips needed for the initial sample transfer. \n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify the number of samples to run.\n Sample Plate (input) Type: Select the type of plate used.\n Extraction Plate (MagPlate) Type: Select the type of plate used.\n Elution Plate (output) Type: Select the type of plate used.\n P300-Multi Mount: Select which mount (left, right) the P300-Multi is attached to.\n Tip Type: Specify the type of tips (filtered, non-filtered) used.\n* Used Tips Destination: Specify the destination of used tips. \"Empty Tipracks\" is best suited for runs of more than 24 samples.", "internal": "18d6a1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/18e62e/README.json b/protoBuilds/18e62e/README.json index 5f5158b14..06c56bb7d 100644 --- a/protoBuilds/18e62e/README.json +++ b/protoBuilds/18e62e/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates a Multiplex LDT 384-Well Plate PCR prep. Using up to four KingFisher 96-Well Plates as inputs and an Opentrons Temperature Module to keep reagents cool, this protocol transfers water, primer/probes, and master mix to necessary wells in 384-Well Plate before transferring samples from the KingFisher plates.\nThis protocol is still a work in progress and will be updated.\nUpdate 2021-10-25: A new parameter was added (Only Transfer Samples) that will skip the addition of reaction mix components and use of the temperature module; instead, simply transferring samples from 96-well plates to 384-well plate.\nExplanation of complex parameters below:\n* Plate 1 Number of Samples: Specify the number of samples in Plate 1 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* Plate 2 Number of Samples: Specify the number of samples in Plate 2 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* Plate 3 Number of Samples: Specify the number of samples in Plate 3 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* Plate 4 Number of Samples: Specify the number of samples in Plate 4 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* Pipette Mount: Select which mount the P20 Multi-Channel Pipette (GEN2) is attached to.\n* Used Tip Location: Select where used tips should be dropped after transferring samples. Empty Tip Rack is recommended due to space constraints in the waste bin.\n", + "description": "This protocol automates a Multiplex LDT 384-Well Plate PCR prep. Using up to four KingFisher 96-Well Plates as inputs and an Opentrons Temperature Module to keep reagents cool, this protocol transfers water, primer/probes, and master mix to necessary wells in 384-Well Plate before transferring samples from the KingFisher plates.\nThis protocol is still a work in progress and will be updated.\nUpdate 2021-10-25: A new parameter was added (Only Transfer Samples) that will skip the addition of reaction mix components and use of the temperature module; instead, simply transferring samples from 96-well plates to 384-well plate.\nExplanation of complex parameters below:\n Plate 1 Number of Samples: Specify the number of samples in Plate 1 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n Plate 2 Number of Samples: Specify the number of samples in Plate 2 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n Plate 3 Number of Samples: Specify the number of samples in Plate 3 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n Plate 4 Number of Samples: Specify the number of samples in Plate 4 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n Pipette Mount: Select which mount the P20 Multi-Channel Pipette (GEN2) is attached to.\n Used Tip Location: Select where used tips should be dropped after transferring samples. Empty Tip Rack is recommended due to space constraints in the waste bin.\n", "internal": "18e62e", "labware": "\nOpentrons 20\u00b5L Filter Tips\nKingFisher 96-Deepwell Plate\nMicroAmp\u2122 EnduraPlate\u2122 Optical 384-Well Plate\nOpentrons 96-Well Aluminum Block + PCR Strips (200\u00b5L)\n", "markdown": { diff --git a/protoBuilds/19313a/README.json b/protoBuilds/19313a/README.json index 80c82bae9..28b8bba65 100644 --- a/protoBuilds/19313a/README.json +++ b/protoBuilds/19313a/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol extracts RNA with a temperature module and magnetic module. User has the choice to include a \"Waste water mode\" which consists of adding and mixing binding buffer on magnetically engaged beads. Tips are tracked between protocols with the protocol pausing and prompting the user to replace tip racks when a tip rack is depleted.\nExplanation of complex parameters below:\n* Most customizable variables below are in reference to the original protocol request coded by the user. All additional parameters are explained:\n* Reset Tipracks: Select yes to pick up the tip from A1 on both the 200ul and 300ul tip racks. Select no to pick up the tips for both tip racks from where the previous run left off.\n* Remove supernatant aspiration height (mm): Select aspiration height from the bottom of the well to remove supernatant.\n* Length from side of the well opposite magnetically engaged beads (mm): Specify the distance to aspirate from the side of the well opposite the magnetically engaged beads. A values of 1 is the side of the well, a values of 4.1 is the middle of the well.\n* P300 Single GEN2 Mount: Select which side (left or right) to mount P300 single channel pipette.\n", + "description": "This protocol extracts RNA with a temperature module and magnetic module. User has the choice to include a \"Waste water mode\" which consists of adding and mixing binding buffer on magnetically engaged beads. Tips are tracked between protocols with the protocol pausing and prompting the user to replace tip racks when a tip rack is depleted.\nExplanation of complex parameters below:\n Most customizable variables below are in reference to the original protocol request coded by the user. All additional parameters are explained:\n Reset Tipracks: Select yes to pick up the tip from A1 on both the 200ul and 300ul tip racks. Select no to pick up the tips for both tip racks from where the previous run left off.\n Remove supernatant aspiration height (mm): Select aspiration height from the bottom of the well to remove supernatant.\n Length from side of the well opposite magnetically engaged beads (mm): Specify the distance to aspirate from the side of the well opposite the magnetically engaged beads. A values of 1 is the side of the well, a values of 4.1 is the middle of the well.\n* P300 Single GEN2 Mount: Select which side (left or right) to mount P300 single channel pipette.\n", "internal": "19313a", "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 4-in-1 Tube Rack Set\nOpentrons 200uL Filter Tips\nOpentrons 300uL Tips\n", "markdown": { diff --git a/protoBuilds/19fc32/README.json b/protoBuilds/19fc32/README.json index 5c611b3d7..2c2dadb03 100644 --- a/protoBuilds/19fc32/README.json +++ b/protoBuilds/19fc32/README.json @@ -5,7 +5,7 @@ "Clean Up" ] }, - "description": "This protocol is a slightly modified version of a clean up protocol. With this protocol, the user selects which mount their P50-Multi is attached to and the protocol adds the necessary reagents and (dis)engages the magnetic module to accomplish the clean up. To conclude this protocol, 4\u00b5L of supernatant is added to a 384-well plate and 20\u00b5L of supernatant is added to a 96-well plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P50 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nBio-Rad 96-Well Plate, 200\u00b5L\nBio-Rad 384-Well Plate\nNEST 12-Well Reservoir\nReagents\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n* A1: Magnetic Beads\n* A2: 80% Fresh Ethanol (~10mL)\n* A3: 80% Fresh Ethanol (~10mL)\n* A4: 80% Fresh Ethanol (~10mL)\n* A5: 80% Fresh Ethanol (~10mL)\n* A6: RSB Buffer\n* A7: Empty\n* A8: Empty\n* A9: Empty, for liquid waste\n* A10: Empty, for liquid waste\n* A11: Empty, for liquid waste\n* A12: Empty, for liquid waste\nSlot 2: Bio-Rad 96-Well Plate, clean and empty\nSlot 3: Bio-Rad 384-Well Plate\nSlot 4: Opentrons Magnetic Module with a Bio-Rad 96-Well Plate, filled with 25\u00b5L of sample\nSlot 5: Opentrons 50/300\u00b5L Tips\nSlot 6: Opentrons 50/300\u00b5L Tips\nSlot 7: Opentrons 50/300\u00b5L Tips\nSlot 8: Opentrons 50/300\u00b5L Tips\nSlot 9: Opentrons 50/300\u00b5L Tips\nSlot 10: Opentrons 50/300\u00b5L Tips\nUsing the customizations fields, below set up your protocol.\n* P50 Multi Mount: Select which mount (left or right) the P50 Multi is attached to.", + "description": "This protocol is a slightly modified version of a clean up protocol. With this protocol, the user selects which mount their P50-Multi is attached to and the protocol adds the necessary reagents and (dis)engages the magnetic module to accomplish the clean up. To conclude this protocol, 4\u00b5L of supernatant is added to a 384-well plate and 20\u00b5L of supernatant is added to a 96-well plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P50 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nBio-Rad 96-Well Plate, 200\u00b5L\nBio-Rad 384-Well Plate\nNEST 12-Well Reservoir\nReagents\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n A1: Magnetic Beads\n A2: 80% Fresh Ethanol (~10mL)\n A3: 80% Fresh Ethanol (~10mL)\n A4: 80% Fresh Ethanol (~10mL)\n A5: 80% Fresh Ethanol (~10mL)\n A6: RSB Buffer\n A7: Empty\n A8: Empty\n A9: Empty, for liquid waste\n A10: Empty, for liquid waste\n A11: Empty, for liquid waste\n A12: Empty, for liquid waste\nSlot 2: Bio-Rad 96-Well Plate, clean and empty\nSlot 3: Bio-Rad 384-Well Plate\nSlot 4: Opentrons Magnetic Module with a Bio-Rad 96-Well Plate, filled with 25\u00b5L of sample\nSlot 5: Opentrons 50/300\u00b5L Tips\nSlot 6: Opentrons 50/300\u00b5L Tips\nSlot 7: Opentrons 50/300\u00b5L Tips\nSlot 8: Opentrons 50/300\u00b5L Tips\nSlot 9: Opentrons 50/300\u00b5L Tips\nSlot 10: Opentrons 50/300\u00b5L Tips\nUsing the customizations fields, below set up your protocol.\n* P50 Multi Mount: Select which mount (left or right) the P50 Multi is attached to.", "internal": "19fc32", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1a2343/README.json b/protoBuilds/1a2343/README.json index 672b3a4a1..32329750f 100644 --- a/protoBuilds/1a2343/README.json +++ b/protoBuilds/1a2343/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol performs a custom PCR preparation for gel samples using an on-deck Opentrons Thermocycler module.\n\n\n\nOpentrons Thermocycler (occupying slots 7, 8, 10, 11) with NEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons Temperature Module with USA Scientific 96 Deep Well Plate 2.4 mL\nCorning 96 Well Plate 360 \u00b5L Flat\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\n96-deepwell reagent block on temperature module (slot 4)\n* well A1: DNTPs\n* well B1: polymerase\n* column 2: PCR buffer\n* wells A3-H3: templates 1-8\n* column 4: water", + "description": "This protocol performs a custom PCR preparation for gel samples using an on-deck Opentrons Thermocycler module.\n\n\n\nOpentrons Thermocycler (occupying slots 7, 8, 10, 11) with NEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons Temperature Module with USA Scientific 96 Deep Well Plate 2.4 mL\nCorning 96 Well Plate 360 \u00b5L Flat\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\n96-deepwell reagent block on temperature module (slot 4)\n well A1: DNTPs\n well B1: polymerase\n column 2: PCR buffer\n wells A3-H3: templates 1-8\n* column 4: water", "internal": "1a2343", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1adec6-2/README.json b/protoBuilds/1adec6-2/README.json index e056e4a10..f2e11fe9d 100644 --- a/protoBuilds/1adec6-2/README.json +++ b/protoBuilds/1adec6-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: Destination Plate 1 (SPL 96-Well Cell Culture Plate)\n\nSlot 2: Destination Plate 2 (SPL 96-Well Cell Culture Plate)\n\nSlot 3: Destination Plate 3 (SPL 96-Well Cell Culture Plate)\n\nSlot 4: NEST 12-Well Reservoir, 15mL\n\nSlot 7: Opentrons 300\u00b5L Tiprack\n", - "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part two of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, 250\u00b5L of cells are transferred from the NEST 12-Well Reservoir, 15mL to the SPL 96-Well Cell Culture Plates.\nExplanation of complex parameters below:\n* P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n* Number of Destination Plates: Select the number of destination plates.\n", + "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part two of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, 250\u00b5L of cells are transferred from the NEST 12-Well Reservoir, 15mL to the SPL 96-Well Cell Culture Plates.\nExplanation of complex parameters below:\n P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n Number of Destination Plates: Select the number of destination plates.\n", "internal": "1adec6-2", "labware": "\nOpentrons 300\u00b5L Tipracks\nNEST 12-Well Reservoir, 15mL\nSPL 96-Well Cell Culture Plates (Round Bottom)\n", "markdown": { diff --git a/protoBuilds/1adec6-3/README.json b/protoBuilds/1adec6-3/README.json index 0db0c4ffa..9b14c8aed 100644 --- a/protoBuilds/1adec6-3/README.json +++ b/protoBuilds/1adec6-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: Destination Plate 1 (SPL 96-Well Cell Culture Plat)\n\nSlot 2: Destination Plate 2 (SPL 96-Well Cell Culture Plate)\n\nSlot 3: Destination Plate 3 (SPL 96-Well Cell Culture Plate)\n\nSlot 4: Opentrons 20\u00b5L Tiprack\n\nSlot 5: Opentrons 300\u00b5L Tiprack (optional, for mixing)\n\nSlot 6: Small Molecule Library Plate (Thermo-Fast 96-Well, Fully Skirted Plate)\n\nSlot 7: Opentrons 20\u00b5L Tiprack\n\nSlot 8: Opentrons 300\u00b5L Tiprack (optional, for mixing)\n\nSlot 10: Opentrons 20\u00b5L Tiprack\n\nSlot 11: Opentrons 300\u00b5L Tiprack (optional, for mixing)\n\n", - "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part three of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, 1\u00b5L is transferred from the small molecule library plate to the experiment plate seeded with cells.\nExplanation of complex parameters below:\n* P20-Multi Mount: Select which mount the P20-Multi Pipette is attached to.\n* Number of Destination Plates: Select the number of destination plates.\n* Transfer volume (in \u00b5L): Specify the volume to be transferred.\n* Mix with P300-Multi: Select whether or not to add an optional mix step with the P300-Multi Pipette (200\u00b5L, 3 times) after the transfer occurs\n", + "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part three of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, 1\u00b5L is transferred from the small molecule library plate to the experiment plate seeded with cells.\nExplanation of complex parameters below:\n P20-Multi Mount: Select which mount the P20-Multi Pipette is attached to.\n Number of Destination Plates: Select the number of destination plates.\n Transfer volume (in \u00b5L): Specify the volume to be transferred.\n Mix with P300-Multi: Select whether or not to add an optional mix step with the P300-Multi Pipette (200\u00b5L, 3 times) after the transfer occurs\n", "internal": "1adec6-3", "labware": "\nOpentrons 20\u00b5L Tipracks\n\n\nOpentrons 300\u00b5L Tipracks (optional)\n\n\nThermo-Fast 96-Well, Fully Skirted Plate\nSPL 96-Well Cell Culture Plates\n", "markdown": { diff --git a/protoBuilds/1adec6-4/README.json b/protoBuilds/1adec6-4/README.json index 29d7ff24d..08e05cfc4 100644 --- a/protoBuilds/1adec6-4/README.json +++ b/protoBuilds/1adec6-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: Small Molecule Library Plate (Thermo-Fast 96-Well, Fully Skirted Plate)\n\nSlot 2: Destination Plate (SPL 96-Well Cell Culture Plate)\n\nSlot 3: Opentrons 300\u00b5L Tiprack\n\nSlot 4: Opentrons 20\u00b5L Tiprack\n\nSlot 5: Opentrons 20\u00b5L Tiprack\n\nSlot 7: Opentrons 20\u00b5L Tiprack\n\nSlot 8: Opentrons 20\u00b5L Tiprack\n\nSlot 10: Opentrons 20\u00b5L Tiprack\n\nSlot 11: Opentrons 20\u00b5L Tiprack\n\n", - "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part four of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, a CSV is used to dictate the volume and destination of liquid transfers using the P20 Single-Channel Pipette (GEN2).\nExplanation of complex parameters below:\n* P20 Mount: Select which mount the P20 Pipette is attached to.\n* P20 Selection (Single or Multi): Select which pipette is used (please see note below)\n* Transfer CSV: Upload the CSV containing the liquid transfers. The CSV should be formatted as follows:\n\n| Source Well | Volume | Destination Well |\n| ----------- | ------ | ---------------- |\n| A1 | 3 | C2 |\n| A1 | 2 | B4 |\n| A2 | 5 | D7 |\nNote: If using the P20 Multi-Channel Pipette (GEN2), you should only use Row A when selecting a destination well in the CSV.\n", + "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part four of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, a CSV is used to dictate the volume and destination of liquid transfers using the P20 Single-Channel Pipette (GEN2).\nExplanation of complex parameters below:\n P20 Mount: Select which mount the P20 Pipette is attached to.\n P20 Selection (Single or Multi): Select which pipette is used (please see note below)\n* Transfer CSV: Upload the CSV containing the liquid transfers. The CSV should be formatted as follows:\n\n| Source Well | Volume | Destination Well |\n| ----------- | ------ | ---------------- |\n| A1 | 3 | C2 |\n| A1 | 2 | B4 |\n| A2 | 5 | D7 |\nNote: If using the P20 Multi-Channel Pipette (GEN2), you should only use Row A when selecting a destination well in the CSV.\n", "internal": "1adec6-4", "labware": "\nOpentrons 20\u00b5L Tipracks\nOpentrons 300\u00b5L Tipracks\nThermo-Fast 96-Well, Fully Skirted Plate\nSPL 96-Well Cell Culture Plates\n", "markdown": { diff --git a/protoBuilds/1adec6-5/README.json b/protoBuilds/1adec6-5/README.json index a89a9d988..f316469bc 100644 --- a/protoBuilds/1adec6-5/README.json +++ b/protoBuilds/1adec6-5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: Source Plate, containing Cells (SPL 96-Well Cell Culture Plate)\n\nSlot 4: Destination Plate (SPL 96-Well Cell Culture Plate)\n\nSlot 5: Optional, Second Destination Plate (SPL 96-Well Cell Culture Plate)\n\nSlot 6: [NEST 12-Well Reservoir, 15mL\n\nSlot 7: Opentrons 300\u00b5L Tiprack\n", - "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part five of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, the P300 8-Channel Pipette (GEN2) transfers 220\u00b5L of supernatant from source plate containing cells to a destination plate. Once complete, the P300 8-Channel Pipette (GEN2) will transfer 100\u00b5L of Cell medium+10% PrestoBlue to the original source plate.\nExplanation of complex parameters below:\n* P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n* Aspirate from Well Bottom Height: Specify the height from the bottom of the well (in mm) that the pipette will aspirate supernatant (note: default height is 1mm from bottom).\n* Perform 2nd aliquot: Specify whether or not to perform a second aliquot (110\u00b5L transferred to plate in slot 5)\n", + "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part five of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nIn this protocol, the P300 8-Channel Pipette (GEN2) transfers 220\u00b5L of supernatant from source plate containing cells to a destination plate. Once complete, the P300 8-Channel Pipette (GEN2) will transfer 100\u00b5L of Cell medium+10% PrestoBlue to the original source plate.\nExplanation of complex parameters below:\n P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n Aspirate from Well Bottom Height: Specify the height from the bottom of the well (in mm) that the pipette will aspirate supernatant (note: default height is 1mm from bottom).\n* Perform 2nd aliquot: Specify whether or not to perform a second aliquot (110\u00b5L transferred to plate in slot 5)\n", "internal": "1adec6-5", "labware": "\nOpentrons 300\u00b5L Tipracks\nSPL 96-Well Cell Culture Plates\nNEST 12-Well Reservoir, 15mL\n", "markdown": { diff --git a/protoBuilds/1adec6-6/README.json b/protoBuilds/1adec6-6/README.json index 37ba8028c..ed74beb96 100644 --- a/protoBuilds/1adec6-6/README.json +++ b/protoBuilds/1adec6-6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: Optional, Destination Plate 2 (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 2: Optional, Sample Plate 2 (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 3: NEST 12-Well Reservoir, 15mL\n\nSlot 4: Destination Plate 1 (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 5: Sample Plate 1 (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 6: Standards Plate (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 7: Opentrons 300\u00b5L Tiprack\n\nSlot 8: Opentrons 300\u00b5L Tiprack\n\nSlot 10: Opentrons 300\u00b5L Tiprack\n", - "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part six of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nThis protocol is the first half of a custom, ProcartaPlex protocol. In this protocol, 50\u00b5L of Magnetic Beads are added to all the wells of the Destination Plate. The user is then prompted to remove the plate and incubate off the deck before returning to the robot. Once the Destination Plate is replaced, Wash Buffer is added and then 50\u00b5L of samples (columns 1-10 of Sample Plate) and standards (columns 1 and 2 of Standards Plate) are added to the Destination Plate. The user is then prompted to perform some off-deck steps before incubating overnight. Once incubation is complete, users can move on to ProcartaPlex Protocol-2.\nExplanation of complex parameters below:\n* P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n* Number of destination plates: Select how many destination plates will be used in the protocol (1 or 2).\n", + "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part six of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nThis protocol is the first half of a custom, ProcartaPlex protocol. In this protocol, 50\u00b5L of Magnetic Beads are added to all the wells of the Destination Plate. The user is then prompted to remove the plate and incubate off the deck before returning to the robot. Once the Destination Plate is replaced, Wash Buffer is added and then 50\u00b5L of samples (columns 1-10 of Sample Plate) and standards (columns 1 and 2 of Standards Plate) are added to the Destination Plate. The user is then prompted to perform some off-deck steps before incubating overnight. Once incubation is complete, users can move on to ProcartaPlex Protocol-2.\nExplanation of complex parameters below:\n P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n Number of destination plates: Select how many destination plates will be used in the protocol (1 or 2).\n", "internal": "1adec6-6", "labware": "\nOpentrons 300\u00b5L Tipracks\nProcartaPlex 96-Well Cell Culture Plates\nNEST 12-Well Reservoir, 15mL\n", "markdown": { diff --git a/protoBuilds/1adec6-7/README.json b/protoBuilds/1adec6-7/README.json index e3031cfd9..48c5c4683 100644 --- a/protoBuilds/1adec6-7/README.json +++ b/protoBuilds/1adec6-7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: NEST 12-Well Reservoir, 15mL\n\nSlot 2: Optional, NEST 12-Well Reservoir, 15mL (2)\n\nSlot 3: Optional, NEST 12-Well Reservoir, 15mL (3)\n\nSlot 4: Destination Plate (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 5: Optional, Destination Plate (2) (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 6: Optional, Destination Plate (3) (ProcartaPlex 96-Well Cell Culture Plate)\n\nSlot 7: Opentrons 300\u00b5L Tiprack\n", - "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part seven of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nThis protocol is the second half of a custom, ProcartaPlex protocol - the first half can be found here. This protocol begins after the overnight incubation from the first half with two wash steps. After the washes, 25\u00b5L of Detection Antibodies are added to the wells and the user is prompted to remove the plate for off-deck processing. Once the plate is returned, two more wash steps occur. Once the washes are complete, 50\u00b5L of SAP is added to the wells and the user is again prompted to remove the deck for off-deck processing. Once the plate is returned, the final two wash steps occur, before 120\u00b5L of Reading Buffer is added to the wells - completing the automated portion of this workflow.\nExplanation of complex parameters below:\n* P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n* Number of destination plates: Select how many destination plates will be used in the protocol (1, 2, or 3).\n", + "description": "Updated\nThis protocol has been updated based on feedback from the user.\n\nThis protocol is part seven of a larger workflow. The entire workflow can be found below\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\n\nThis protocol is the second half of a custom, ProcartaPlex protocol - the first half can be found here. This protocol begins after the overnight incubation from the first half with two wash steps. After the washes, 25\u00b5L of Detection Antibodies are added to the wells and the user is prompted to remove the plate for off-deck processing. Once the plate is returned, two more wash steps occur. Once the washes are complete, 50\u00b5L of SAP is added to the wells and the user is again prompted to remove the deck for off-deck processing. Once the plate is returned, the final two wash steps occur, before 120\u00b5L of Reading Buffer is added to the wells - completing the automated portion of this workflow.\nExplanation of complex parameters below:\n P300-Multi Mount: Select which mount the P300-Multi Pipette is attached to.\n Number of destination plates: Select how many destination plates will be used in the protocol (1, 2, or 3).\n", "internal": "1adec6-7", "labware": "\nOpentrons 300\u00b5L Tipracks\nProcartaPlex 96-Well Cell Culture Plates\nNEST 12-Well Reservoir, 15mL\n", "markdown": { diff --git a/protoBuilds/1adec6/README.json b/protoBuilds/1adec6/README.json index c7c0d05f0..1b389fab9 100644 --- a/protoBuilds/1adec6/README.json +++ b/protoBuilds/1adec6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: Aliquot Plate 1 (Thermo-Fast 96-Well, Fully Skirted Plates)\n\nSlot 2: Aliquot Plate 2 (Thermo-Fast 96-Well, Fully Skirted Plates)\n\nSlot 3: Aliquot Plate 3 (Thermo-Fast 96-Well, Fully Skirted Plates)\n\nSlot 4: Sample Plate (Thermo-Fast 96-Well, Fully Skirted Plate)\n\nSlot 5: Destination Plate (Thermo-Fast 96-Well, Fully Skirted Plate)\n\nSlot 6: NEST 12-Well Reservoir, 15mL\n\nSlot 7: Opentrons 20\u00b5L Tiprack\n\nSlot 8: Opentrons 20\u00b5L Tiprack\n", - "description": "This protocol now utilizes the P20 8-Channel Pipette (GEN2) (instead of the P300), uses additional plates, and has modified liquid handling. The steps of this updated version can be found below.\nUpdated Sept 29, 2021\nThis protocol has been updated based on feedback from the user. User can now select None when selecting a \"Number of Destination Plates\" (skipping the aliquoting step). Additionally, this update fixes an issue with the way tips are handled when using less than 8 tips with the multi-channel pipette.\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\nExplanation of complex parameters below:\n* P20-Multi Mount: Select which mount the P20-Multi Pipette is attached to.\n* Number of Destination Plates: Select the number of destination plates.\n* Destination plate PBS volume (\u00b5l): Specify the volume of PBS to transfer to Destination plate (step 1).\n* Destination plate 66% DMSO volume (\u00b5l): Specify the volume of 66% DMSO to transfer to Destination plate (step 2).\n* Source plate volume for dilution (\u00b5l): Specify the volume for first dilution transfer (step 3).\n* Destination plate volume for dilution (\u00b5l): Specify the volume for second dilution transfer (step 5).\n* Library aliquot volume (\u00b5l): Specify the volume for the library aliquot (step 7).\n", + "description": "This protocol now utilizes the P20 8-Channel Pipette (GEN2) (instead of the P300), uses additional plates, and has modified liquid handling. The steps of this updated version can be found below.\nUpdated Sept 29, 2021\nThis protocol has been updated based on feedback from the user. User can now select None when selecting a \"Number of Destination Plates\" (skipping the aliquoting step). Additionally, this update fixes an issue with the way tips are handled when using less than 8 tips with the multi-channel pipette.\nPart 1: Small Molecule Library Prep\nPart 2: Seed Cells\nPart 3: Transfer Small Molecules\nPart 4: Transfer Small Molecules - CSV Input\nPart 5: Custom Supernatant Removal\nPart 6: ProcartaPlex Protocol-1\nPart 7: ProcartaPlex Protocol-2\nExplanation of complex parameters below:\n P20-Multi Mount: Select which mount the P20-Multi Pipette is attached to.\n Number of Destination Plates: Select the number of destination plates.\n Destination plate PBS volume (\u00b5l): Specify the volume of PBS to transfer to Destination plate (step 1).\n Destination plate 66% DMSO volume (\u00b5l): Specify the volume of 66% DMSO to transfer to Destination plate (step 2).\n Source plate volume for dilution (\u00b5l): Specify the volume for first dilution transfer (step 3).\n Destination plate volume for dilution (\u00b5l): Specify the volume for second dilution transfer (step 5).\n* Library aliquot volume (\u00b5l): Specify the volume for the library aliquot (step 7).\n", "internal": "1adec6", "labware": "\nOpentrons 20\u00b5L Tipracks\nNEST 12-Well Reservoir, 15mL\nThermo-Fast 96-Well, Fully Skirted Plates\n", "markdown": { diff --git a/protoBuilds/1b2788/README.json b/protoBuilds/1b2788/README.json index fc46b9c7d..4b4bc3d7c 100644 --- a/protoBuilds/1b2788/README.json +++ b/protoBuilds/1b2788/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs the Zymo Quick-DNA Fecal/Soil Microbe 96 Magbead Kit. Please find a description of the kit below from Zymo's website:\nThe Quick-DNA Fecal/Soil Microbe 96 Magbead Kits are designed for the simple and rapid isolation of inhibitor-free, PCR-quality host cell and microbial DNA from a variety of sample sources, including humans, birds, rats, mice, cattle, etc. The procedure is easy and can be completed in as little as 90 minutes: fecal samples are rapidly and efficiently lysed by bead beating with our state of the art, ultra-high density BashingBeads. Zymo MagBinding Bead technology, which features Zymo Research's Inhibitor Removal technology, is then used to isolate the DNA. Eluted DNA is ideal for downstream molecular-based applications including PCR, arrays, genotyping, methylation detection, etc.\nExplanation of complex parameters below:\n* Number of Columns: Specify the number of sample columns in this run (1-12).\n* Pre-Wash buffer volume (ul): Specify wash volumes for both the pre-wash buffer, and gDNA wash buffer in microliters. Volumes can be greater than 200ul, and will be split if need be over multiple transfers.\n* Magnetic Module Engage Height: Specify the magnetic module engage height in mm.\n* Elute Buffer Volume: Specify the elute buffer volume in microliters.\n* P300 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", + "description": "This protocol performs the Zymo Quick-DNA Fecal/Soil Microbe 96 Magbead Kit. Please find a description of the kit below from Zymo's website:\nThe Quick-DNA Fecal/Soil Microbe 96 Magbead Kits are designed for the simple and rapid isolation of inhibitor-free, PCR-quality host cell and microbial DNA from a variety of sample sources, including humans, birds, rats, mice, cattle, etc. The procedure is easy and can be completed in as little as 90 minutes: fecal samples are rapidly and efficiently lysed by bead beating with our state of the art, ultra-high density BashingBeads. Zymo MagBinding Bead technology, which features Zymo Research's Inhibitor Removal technology, is then used to isolate the DNA. Eluted DNA is ideal for downstream molecular-based applications including PCR, arrays, genotyping, methylation detection, etc.\nExplanation of complex parameters below:\n Number of Columns: Specify the number of sample columns in this run (1-12).\n Pre-Wash buffer volume (ul): Specify wash volumes for both the pre-wash buffer, and gDNA wash buffer in microliters. Volumes can be greater than 200ul, and will be split if need be over multiple transfers.\n Magnetic Module Engage Height: Specify the magnetic module engage height in mm.\n Elute Buffer Volume: Specify the elute buffer volume in microliters.\n* P300 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", "internal": "1b2788", "labware": "\nOpentrons 200ul Filter tips\nNEST 12-Well Reservoirs, 15 mL\nNEST 1-Well Reservoirs, 195 mL\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nZymo 96 well plate 1.2mL\n", "markdown": { diff --git a/protoBuilds/1c3611/README.json b/protoBuilds/1c3611/README.json index ded092bc8..ba6a1b8f8 100644 --- a/protoBuilds/1c3611/README.json +++ b/protoBuilds/1c3611/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs a custom 384-well PCR preparation. The user has the option to enter the following parameters:\n* number of samples\n* volume of sample\n* number of mastermixes\n* volume of mastermix\n* number of replicates per sample + mastermix combination\nMastermixes should be pre-mixed and loaded into individual tubes as shown below. For efficiency, the mastermixes will first be plated from their source tubes into distribution columns using a single channel pipette, before being loaded into the 384-well plate with an 8-channel pipette.\nFor sample traceability, an output .csv file will be written to the robot's Jupyter notebook server for each protocol run. The user has the option to input a run ID to distinguish each run. To find these output files, please refer to this support article.", + "description": "This protocol performs a custom 384-well PCR preparation. The user has the option to enter the following parameters:\n number of samples\n volume of sample\n number of mastermixes\n volume of mastermix\n* number of replicates per sample + mastermix combination\nMastermixes should be pre-mixed and loaded into individual tubes as shown below. For efficiency, the mastermixes will first be plated from their source tubes into distribution columns using a single channel pipette, before being loaded into the 384-well plate with an 8-channel pipette.\nFor sample traceability, an output .csv file will be written to the robot's Jupyter notebook server for each protocol run. The user has the option to input a run ID to distinguish each run. To find these output files, please refer to this support article.", "internal": "1c3611", "labware": "\nOpentrons 24 Tube Rack with Eppendorf 2 mL Safe-Lock Snapcap\nCorning 384 Well Plate 112 \u00b5L Flat #3640\nBio-Rad 96 Well Plate 200 \u00b5L PCR #hsp9601\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { diff --git a/protoBuilds/1c8468/README.json b/protoBuilds/1c8468/README.json index edea36450..c07f998ef 100644 --- a/protoBuilds/1c8468/README.json +++ b/protoBuilds/1c8468/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol transfers samples from a source plate to one of two target plates (to later undergo PCR) as specified in the uploaded CSV file. Samples from each well in the source plate are distributed to its corresponding target plate 6 columns apart. In the case that one of the target plates is filled, the user is prompted to replace it and resume the protocol. In the case that the source plate is depleted, the user is prompted to replace the source plate and upload its respective CSV file to this webpage, download, and run again. In the latter case, the OT-2 \"remembers\" what wells on the target plate are already filled when a new source plate is introduced (unless user resets the counter - see below). User will also be prompted to replace tip racks during a run if applicable.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Single Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoScientific 96-well Plate 200\u00b5l\n\n\n\nFor this protocol, be sure that the pipettes (P20 and P300) are attached.\nUsing the customization fields below, set up your protocol.\n* Source Plate CSV: Upload a CSV corresponding with the source plate loaded onto the deck.\n* Transfer Volume: Specify the volume (\u00b5L) desired for each well in target plates\n* P20 Single Mount: Specify which mount the P10 is on (left or right).\n* Reset Counter: Reset the counter if running with empty target plates. Do not reset the counter if wells in target plate from last run are to be tracked.\nNote about CSV\nThe CSV should be formatted like so:\nSamples ID | Sample Type | ct_value | Plate Name (ex. A:1) | Plate Position | Target Plate (25 or 30) | Transfer (\"done\" or leave blank)\nThe first row should contain headers (like above). All of the following rows should just have the necessary information.\nLabware Setup\nSlots 1: Custom Endura Source Plate on Opentrons 96 well Aluminum Block\nSlot 2: ThermoScientific 96-well 25-Cycle Target Plate\nSlot 4: ThermoScientific 96-well 30-Cycle Target Plate\nSlot 5: Opentrons 96 Filter Tip Rack 20 \u00b5L", + "description": "This protocol transfers samples from a source plate to one of two target plates (to later undergo PCR) as specified in the uploaded CSV file. Samples from each well in the source plate are distributed to its corresponding target plate 6 columns apart. In the case that one of the target plates is filled, the user is prompted to replace it and resume the protocol. In the case that the source plate is depleted, the user is prompted to replace the source plate and upload its respective CSV file to this webpage, download, and run again. In the latter case, the OT-2 \"remembers\" what wells on the target plate are already filled when a new source plate is introduced (unless user resets the counter - see below). User will also be prompted to replace tip racks during a run if applicable.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Single Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoScientific 96-well Plate 200\u00b5l\n\n\n\nFor this protocol, be sure that the pipettes (P20 and P300) are attached.\nUsing the customization fields below, set up your protocol.\n Source Plate CSV: Upload a CSV corresponding with the source plate loaded onto the deck.\n Transfer Volume: Specify the volume (\u00b5L) desired for each well in target plates\n P20 Single Mount: Specify which mount the P10 is on (left or right).\n Reset Counter: Reset the counter if running with empty target plates. Do not reset the counter if wells in target plate from last run are to be tracked.\nNote about CSV\nThe CSV should be formatted like so:\nSamples ID | Sample Type | ct_value | Plate Name (ex. A:1) | Plate Position | Target Plate (25 or 30) | Transfer (\"done\" or leave blank)\nThe first row should contain headers (like above). All of the following rows should just have the necessary information.\nLabware Setup\nSlots 1: Custom Endura Source Plate on Opentrons 96 well Aluminum Block\nSlot 2: ThermoScientific 96-well 25-Cycle Target Plate\nSlot 4: ThermoScientific 96-well 30-Cycle Target Plate\nSlot 5: Opentrons 96 Filter Tip Rack 20 \u00b5L", "internal": "1c8468", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1ccd23-station-A/README.json b/protoBuilds/1ccd23-station-A/README.json index 57feb939b..64cbb406a 100644 --- a/protoBuilds/1ccd23-station-A/README.json +++ b/protoBuilds/1ccd23-station-A/README.json @@ -5,7 +5,7 @@ "Sample Plating" ] }, - "description": "This protocol plates samples from custom or standard tuberacks to a NEST 96-deepwell plate. 10\u00b5l proteinase K and 10\u00b5l internal control are then added to each sample. Samples are transferred to the plate first down each column, then across each row (A1, B1, C1, ...H1, A2, B2, C2, etc.)\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Single-Channel Pipette\nOpentrons Filter Tips\nOpentrons 4-in-1 Tube Rack Set or custom tuberack\nNEST 96 Deepwell Plate 2mL\nSample Tubes\n\n\n\n2ml tubeblock on temperature module (slot 1):\n* proteinase K: A1\n* internal control: B1", + "description": "This protocol plates samples from custom or standard tuberacks to a NEST 96-deepwell plate. 10\u00b5l proteinase K and 10\u00b5l internal control are then added to each sample. Samples are transferred to the plate first down each column, then across each row (A1, B1, C1, ...H1, A2, B2, C2, etc.)\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Single-Channel Pipette\nOpentrons Filter Tips\nOpentrons 4-in-1 Tube Rack Set or custom tuberack\nNEST 96 Deepwell Plate 2mL\nSample Tubes\n\n\n\n2ml tubeblock on temperature module (slot 1):\n proteinase K: A1\n internal control: B1", "internal": "generic_station_A", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1ccd23-station-B/README.json b/protoBuilds/1ccd23-station-B/README.json index 3ec3d2a9b..ede79fcff 100644 --- a/protoBuilds/1ccd23-station-B/README.json +++ b/protoBuilds/1ccd23-station-B/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This is a flexible protocol accommodating a wide range of commercial RNA extraction workflows for COVID-19 sample processing. The protocol is broken down into 5 main parts:\n* binding buffer addition to samples\n* bead wash 3x using magnetic module\n* final elution to chilled PCR plate\nLysed samples should be loaded on the magnetic module in a NEST 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons Magnetic Module GEN2\nOpentrons Temperature Module GEN2\nNEST 12 Well Reservoir 15 mL\nNEST 1 Well Reservoir 195 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nNEST 96 Deepwell Plate 2mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 5\n\nReservoir 2: slot 2\n\n", + "description": "This is a flexible protocol accommodating a wide range of commercial RNA extraction workflows for COVID-19 sample processing. The protocol is broken down into 5 main parts:\n binding buffer addition to samples\n bead wash 3x using magnetic module\n* final elution to chilled PCR plate\nLysed samples should be loaded on the magnetic module in a NEST 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons Magnetic Module GEN2\nOpentrons Temperature Module GEN2\nNEST 12 Well Reservoir 15 mL\nNEST 1 Well Reservoir 195 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nNEST 96 Deepwell Plate 2mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 5\n\nReservoir 2: slot 2\n\n", "internal": "covid-19-rna-extraction", "markdown": { "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1ccd23-station-C/README.json b/protoBuilds/1ccd23-station-C/README.json index 2af5f4dac..6ecdc9bec 100644 --- a/protoBuilds/1ccd23-station-C/README.json +++ b/protoBuilds/1ccd23-station-C/README.json @@ -5,7 +5,7 @@ "qPCR Setup" ] }, - "description": "This protocol creates a custom qPCR prep protocol for Covid-19 diagnostics. The input into this protocol is an elution plate of purified RNA, and the output is a PCR plate containing the samples mixed with mastermix.\nUsing a Single-Channel Pipette, this protocol will begin by creating reaction mix in a 2ml tube. The mix is then distributed to a PCR strip. Then, using the Multi-Channel Pipette, samples will be transferred from their plate to the qPCR plate and mixed with the reaction mix.\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons Temperature Module with Aluminum Block Set)\nOpentrons P300 Single-Channel GEN2 Pipette\nOpentrons P20 Multi-Channel GEN2 Pipette\nOpentrons Filter Tips\nNEST PCR Plate containing purified nucleic acid samples\n2ml NEST screwcap tubes or equivalent containing reaction mix(es)\n\n\n\nchilled 24-well aluminum block for 2ml tubes (slot 5):\n\nAllplex 2019-nCoV Assay (17\u00b5l/sample total):\n* reagent 1: 2019-nCov MOM (5\u00b5l/sample)\n* reagent 2: RNase-free water (5\u00b5l/sample)\n* reagent 3: 5X Real-time One-step Buffer (5\u00b5l/sample)\n* reagent 4: Real-time One-step Enzyme (2\u00b5l/sample)\nAllplex SARS-CoV-2 Assay (15\u00b5l/sample total):\n* reagent 1: SARS2 MOM (5\u00b5l/sample)\n* reagent 2: EM8 (5\u00b5l/sample)\n* reagent 3: RNase-free water (5\u00b5l/sample)\nSeegene Real-time One-step RT-PCR:\n* reagent 1: SC2FabR MOM (5\u00b5l/sample)\n* reagent 2: EM8 (5\u00b5l/sample)", + "description": "This protocol creates a custom qPCR prep protocol for Covid-19 diagnostics. The input into this protocol is an elution plate of purified RNA, and the output is a PCR plate containing the samples mixed with mastermix.\nUsing a Single-Channel Pipette, this protocol will begin by creating reaction mix in a 2ml tube. The mix is then distributed to a PCR strip. Then, using the Multi-Channel Pipette, samples will be transferred from their plate to the qPCR plate and mixed with the reaction mix.\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons Temperature Module with Aluminum Block Set)\nOpentrons P300 Single-Channel GEN2 Pipette\nOpentrons P20 Multi-Channel GEN2 Pipette\nOpentrons Filter Tips\nNEST PCR Plate containing purified nucleic acid samples\n2ml NEST screwcap tubes or equivalent containing reaction mix(es)\n\n\n\nchilled 24-well aluminum block for 2ml tubes (slot 5):\n\nAllplex 2019-nCoV Assay (17\u00b5l/sample total):\n reagent 1: 2019-nCov MOM (5\u00b5l/sample)\n reagent 2: RNase-free water (5\u00b5l/sample)\n reagent 3: 5X Real-time One-step Buffer (5\u00b5l/sample)\n reagent 4: Real-time One-step Enzyme (2\u00b5l/sample)\nAllplex SARS-CoV-2 Assay (15\u00b5l/sample total):\n reagent 1: SARS2 MOM (5\u00b5l/sample)\n reagent 2: EM8 (5\u00b5l/sample)\n* reagent 3: RNase-free water (5\u00b5l/sample)\nSeegene Real-time One-step RT-PCR:\n reagent 1: SC2FabR MOM (5\u00b5l/sample)\n reagent 2: EM8 (5\u00b5l/sample)", "internal": "1ccd23", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1ce6aa/README.json b/protoBuilds/1ce6aa/README.json index 4a74d8c3e..05101fc6d 100644 --- a/protoBuilds/1ce6aa/README.json +++ b/protoBuilds/1ce6aa/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol is designed for transferring buffered peptone water to BHI with P300 Multi-Channel Pipette. The user has the ability to select the number of samples to run.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Multi Channel Pipette\nFisherbrand 2-20\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\nReagents\n\n\n\nFor this protocol, be sure that the correct pipette (P300-Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Fisherbrand 2-20\u00b5L Tips\nSlot 2: Simport Scientific 500\u00b5L Tubes in Custom Holder (Source)\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder (Destination)\nUsing the customization fields below, set up your protocol.\n* Pipette Mount: Specify which mount the P300-Multi is on (left or right).\n* Number of Samples: Specify how many samples should be transferred (1-96).\n", + "description": "This protocol is designed for transferring buffered peptone water to BHI with P300 Multi-Channel Pipette. The user has the ability to select the number of samples to run.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Multi Channel Pipette\nFisherbrand 2-20\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\nReagents\n\n\n\nFor this protocol, be sure that the correct pipette (P300-Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Fisherbrand 2-20\u00b5L Tips\nSlot 2: Simport Scientific 500\u00b5L Tubes in Custom Holder (Source)\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder (Destination)\nUsing the customization fields below, set up your protocol.\n Pipette Mount: Specify which mount the P300-Multi is on (left or right).\n Number of Samples: Specify how many samples should be transferred (1-96).\n", "internal": "1ce6aa", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1dec68/README.json b/protoBuilds/1dec68/README.json index 88cd0f7d5..a6278c2f4 100644 --- a/protoBuilds/1dec68/README.json +++ b/protoBuilds/1dec68/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps a 96 well plate with 50ul of sample from a custom 96 tube tube rack. Samples are drawn from the tube rack by column (A1, B1, C1...H1, A2...etc.) and dispensed to the well plate in the same order. The pipette will dispense, and then blowout after dispensing into the well plate. The user has the ability to manipulate the number of samples per run. \nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples (1-96) for this run.\n* P300 Single-Channel Mount: Specify which mount (left or right) to host the P300-single channel pipette.\n", + "description": "This protocol preps a 96 well plate with 50ul of sample from a custom 96 tube tube rack. Samples are drawn from the tube rack by column (A1, B1, C1...H1, A2...etc.) and dispensed to the well plate in the same order. The pipette will dispense, and then blowout after dispensing into the well plate. The user has the ability to manipulate the number of samples per run. \nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples (1-96) for this run.\n P300 Single-Channel Mount: Specify which mount (left or right) to host the P300-single channel pipette.\n", "internal": "1dec68", "labware": "\nBio-Rad 50ul 96 Well Plate\n(Opentrons 300uL tips)[https://shop.opentrons.com/universal-filter-tips/]\nCustom 96 tube rack\n", "markdown": { diff --git a/protoBuilds/1dfebe/README.json b/protoBuilds/1dfebe/README.json index e453d94e0..d42177ef5 100644 --- a/protoBuilds/1dfebe/README.json +++ b/protoBuilds/1dfebe/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps a 96 well plate with urine and enzyme hydrolysis, as well as trichloroacetic acid and dilution buffer. The urine samples in the 4 tube racks exactly mimic the 96 well plate with 15 controls already put in by column. The sample pick-off begins from D2 in the tuberack on slot one, corresponding to H2 of the well plate in slot 3 for dispensing. Delays and pauses are included in the protocol to allow for incubation periods and mix steps.\nExplanation of complex parameters below:\n* Use csv for this run?: Specify whether a csv file will be uploaded for this run. If not, nothing in .CSV File below will be referenced.\n* .CSV File: Upload the csv file for this run. The csv file will map which samples the pipette will visit the bottom of the tube. Wells marked with X will be aspirated from the Sample Aspiration Height parameter (see below). Otherwise, wells marked with O (capital letter O, not zero) will be aspirated from the bottom of the tube. Refer to the csv sample below.\n\n* Number of Samples: Specify the number of samples (1-81) for this run.\n* Tip Withdrawal Speed: Specify the tip withdrawal speed for the tip to leave the urine samples.\n* Sample Aspiration Height (mm): Specify the sample aspiration height (in mm) from the bottom of the urine samples to aspirate from. Any well marked X in the csv, if uploaded will use this height. If the csv is not uploaded, all urine samples will use this height.\n* Sample Aspiration Height (mm): Specify the dispense height from the bottom of the 96 well plate to dispense sample. \n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 single channel pipette.\n", + "description": "This protocol preps a 96 well plate with urine and enzyme hydrolysis, as well as trichloroacetic acid and dilution buffer. The urine samples in the 4 tube racks exactly mimic the 96 well plate with 15 controls already put in by column. The sample pick-off begins from D2 in the tuberack on slot one, corresponding to H2 of the well plate in slot 3 for dispensing. Delays and pauses are included in the protocol to allow for incubation periods and mix steps.\nExplanation of complex parameters below:\n Use csv for this run?: Specify whether a csv file will be uploaded for this run. If not, nothing in .CSV File below will be referenced.\n .CSV File: Upload the csv file for this run. The csv file will map which samples the pipette will visit the bottom of the tube. Wells marked with X will be aspirated from the Sample Aspiration Height parameter (see below). Otherwise, wells marked with O (capital letter O, not zero) will be aspirated from the bottom of the tube. Refer to the csv sample below.\n\n Number of Samples: Specify the number of samples (1-81) for this run.\n Tip Withdrawal Speed: Specify the tip withdrawal speed for the tip to leave the urine samples.\n Sample Aspiration Height (mm): Specify the sample aspiration height (in mm) from the bottom of the urine samples to aspirate from. Any well marked X in the csv, if uploaded will use this height. If the csv is not uploaded, all urine samples will use this height.\n Sample Aspiration Height (mm): Specify the dispense height from the bottom of the 96 well plate to dispense sample. \n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 single channel pipette.\n", "internal": "1dfebe", "labware": "\nOpentrons 4-in-1 Tube Rack\nOpentrons 300uL Tips\nNEST 100ul 96 well plate\n", "markdown": { diff --git a/protoBuilds/1e744e/README.json b/protoBuilds/1e744e/README.json index 8bca7cc68..c3dfbb472 100644 --- a/protoBuilds/1e744e/README.json +++ b/protoBuilds/1e744e/README.json @@ -22,7 +22,7 @@ }, "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "process": "\nUse the protocol parameters on this page to make any needed adjustment to: decision to include or skip the mastermix distribution step (included by default), include or skip the sample transfer step (included by default), the number of input samples (1-384), the labware items to be used, the transfer volume of mastermix (default 15 uL), and well bottom clearances (minimum distance in millimeters between the tip and the bottom of the tube or well).\nUpload your protocol into the OT App.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit \"Run\".\n", - "protocol-steps": "This protocol is for part-2 of a two-step process. The input viral RNA samples for this protocol (up to four elution plates output from part-1) were prepared using:\n* automated OT-2 protocol from the Opentrons Protocol Library - Mag-Bind\u00ae Viral DNA/RNA 96 Kit\n* reagent kit - Omega Mag-Bind\u00ae Viral DNA/RNA 96 Kit - 12 x\nSet up: Be sure to use the left USB port to connect the Temperature Module located in deck slot 1. Be sure to use the right USB port to connect the Temperature Module located in deck slot 3. Precool both temperature modules to 4 degrees C by using settings in the OT app prior to running this protocol. Place up to four sample plates (96-well elution plates from the step 1 - extraction of viral RNA) in deck slots 2, 4, 5, 6 (in that order). Place the mastermix plate (with one column already filled for each full plate of 96 input samples, so there would be four columns filled for 384 input samples - 180 uL mastermix per well if mastermix transfer volume is 15 uL, 120 uL per well if 10 uL). Place the 96-well or 384-well reaction plate on the appropriate aluminum block on the Temperature Module in deck slot 3. Place Opentrons 20 uL filter tips opentrons_96_filtertiprack_20ul in deck slots 7-11.\nThe OT-2 will perform the following steps:\n1. Use the p20 multi to distribute mastermix (15 uL per well by default, optionally 10 uL per well) to the reaction plate (either 96-well or 384-well format) according to the number of input viral RNA samples specified.\n5. Use the p20 multi to transfer (5 uL per well) input viral RNA sample to columns of the reaction plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 Multi-Channel Pipette\nOpentrons Filter Tips for the p20 Pipette\nBioGX XFree Mastermix\n384-well Aluminum Block\n\n\n", + "protocol-steps": "This protocol is for part-2 of a two-step process. The input viral RNA samples for this protocol (up to four elution plates output from part-1) were prepared using:\n automated OT-2 protocol from the Opentrons Protocol Library - Mag-Bind\u00ae Viral DNA/RNA 96 Kit\n reagent kit - Omega Mag-Bind\u00ae Viral DNA/RNA 96 Kit - 12 x\nSet up: Be sure to use the left USB port to connect the Temperature Module located in deck slot 1. Be sure to use the right USB port to connect the Temperature Module located in deck slot 3. Precool both temperature modules to 4 degrees C by using settings in the OT app prior to running this protocol. Place up to four sample plates (96-well elution plates from the step 1 - extraction of viral RNA) in deck slots 2, 4, 5, 6 (in that order). Place the mastermix plate (with one column already filled for each full plate of 96 input samples, so there would be four columns filled for 384 input samples - 180 uL mastermix per well if mastermix transfer volume is 15 uL, 120 uL per well if 10 uL). Place the 96-well or 384-well reaction plate on the appropriate aluminum block on the Temperature Module in deck slot 3. Place Opentrons 20 uL filter tips opentrons_96_filtertiprack_20ul in deck slots 7-11.\nThe OT-2 will perform the following steps:\n1. Use the p20 multi to distribute mastermix (15 uL per well by default, optionally 10 uL per well) to the reaction plate (either 96-well or 384-well format) according to the number of input viral RNA samples specified.\n5. Use the p20 multi to transfer (5 uL per well) input viral RNA sample to columns of the reaction plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 Multi-Channel Pipette\nOpentrons Filter Tips for the p20 Pipette\nBioGX XFree Mastermix\n384-well Aluminum Block\n\n\n", "robot": [ "OT-2" ], diff --git a/protoBuilds/1eeb01/README.json b/protoBuilds/1eeb01/README.json index ed498f431..eae152738 100644 --- a/protoBuilds/1eeb01/README.json +++ b/protoBuilds/1eeb01/README.json @@ -5,7 +5,7 @@ "Nucleic Acid Extraction" ] }, - "description": "This protocol is a custom nucleic acid extraction that begins with the samples in 1.5mL tubes. This protocol utilizes the Opentrons Magnetic Module and the Opentrons Temperature Module for this extraction.\nThe protocol begins by adding 500\u00b5L of Buffer 1 to all tubes that will contain samples on the temperature module. Once complete, 500\u00b5L of sample is transferred from 1.5mL tubes in an Opentrons 4-in-1 Tube Rack to the tubes containing Buffer 1.\nAfter a heating step, DNA and Magnetic Beads are added to the sample tubes on the temperature module and the samples are transferred to a deepwell plate on the magnetic module.\nOnce on the magnetic module, the magnet is engaged and after the beads settle, the supernatant is removed. Using Buffer 2, three consecutive wash steps occur with the samples on the magnetic module.\nAt this point, the user will be prompted to replace the tube(s) in the Tube Rack with Buffer 3 and the Reaction Mix (more info on this below). Buffer 3 will then be added to the beads, mixed with the beads, then transferred back to the temperature module for a 5 minute incubation at 65C.\nPost-incubation, the samples will be moved back to the deepwell plate on the magnetic module, but in a new, clean well. The magnet will engage after all of the samples have been transferred. Following this, the reaction mix will be distributed to all of destinations in PCR strips. The elution will then be transferred to a clean PCR strip, before 5\u00b5L gets transferred to two tubes containing the reaction mix.\nThis concludes the OT-2 portion of the protocol and the user will be prompted to move the samples to 65c for a 20 minute incubation to complete the protocol. \nAdjust the parameters and download the protocol below. \nNote: This protocol is still a work in progress and will likely need further optimizations; please keep this in mind when using this protocol. \n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nP20 Single-Channel Pipette (left mount)\nP300 or P1000 Single-Channel Pipette (right mount)\nOpentrons 20\u00b5L Filter Tips\nOpentrons Filters Tips for P300 or P1000\nOpentrons Magnetic Module, GEN2\nOpentrons Temperature Module, GEN2\nOpentrons 4-in-1 Tube Rack\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nNEST 96-Deepwell Plate, 2mL\nNEST 1.5mL Centrifuge Tubes\nPCR Strips\nReagents\nSamples\n\n\n\nDeck Layout \nSlot 1: Opentrons 96-Well Aluminum Block with PCR Strips\nA1: Magnetic Beads\nB1: DNA\nColumns 2-4: Elution Destination (empty to begin)\nColumns 7-12: Reaction Mix + Elution Destination (empty to begin) \nSlot 2: Opentrons 20\u00b5L Filter Tips \nSlot 3: Opentrons Filters Tips for P300 or P1000 (Tiprack 3) \nSlot 4: Opentrons 4-in-1 Tube Rack with NEST 1.5mL Centrifuge Tubes\nNote: At the beginning of the protocol, samples should be loaded in the tube rack. Once transferred:\nA1: Buffer 3\nA4: Reaction Mix \nSlot 5: Opentrons 20\u00b5L Filter Tips \nSlot 6: Opentrons Filters Tips for P300 or P1000 (Tiprack 2) \nSlot 7: Opentrons Temperature Module, GEN2 with [Opentrons 24-Well Aluminum Block]((https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set) containing NEST 1.5mL Centrifuge Tubes \nSlot 8: NEST 12-Well Reservoir, 15mL\nA1: Buffer 1\nA2: Buffer 2 (Wash 1, Samples 1-12)\nA3: Buffer 2 (Wash 1, Samples 13-24)\nA4: Buffer 2 (Wash 2, Samples 1-12)\nA5: Buffer 2 (Wash 2, Samples 13-24)\nA6: Buffer 2 (Wash 3, Samples 1-12)\nA7: Buffer 2 (Wash 3, Samples 13-24) \nSlot 9: Opentrons Filters Tips for P300 or P1000 (Tiprack 1) \nSlot 10: Opentrons Magnetic Module, GEN2 with NEST 96-Deepwell Plate, 2mL \nSlot 11: NEST 1-Well Reservoir, 195mL (for liquid waste) \nUsing the customizations field (below), set up your protocol.\n* Pipette & Tip Combo: Select which pipette (right mount) and corresponding tips are being used in this protocol.\n* Number of Samples (1-24): Specify the number of samples to run (1-24).", + "description": "This protocol is a custom nucleic acid extraction that begins with the samples in 1.5mL tubes. This protocol utilizes the Opentrons Magnetic Module and the Opentrons Temperature Module for this extraction.\nThe protocol begins by adding 500\u00b5L of Buffer 1 to all tubes that will contain samples on the temperature module. Once complete, 500\u00b5L of sample is transferred from 1.5mL tubes in an Opentrons 4-in-1 Tube Rack to the tubes containing Buffer 1.\nAfter a heating step, DNA and Magnetic Beads are added to the sample tubes on the temperature module and the samples are transferred to a deepwell plate on the magnetic module.\nOnce on the magnetic module, the magnet is engaged and after the beads settle, the supernatant is removed. Using Buffer 2, three consecutive wash steps occur with the samples on the magnetic module.\nAt this point, the user will be prompted to replace the tube(s) in the Tube Rack with Buffer 3 and the Reaction Mix (more info on this below). Buffer 3 will then be added to the beads, mixed with the beads, then transferred back to the temperature module for a 5 minute incubation at 65C.\nPost-incubation, the samples will be moved back to the deepwell plate on the magnetic module, but in a new, clean well. The magnet will engage after all of the samples have been transferred. Following this, the reaction mix will be distributed to all of destinations in PCR strips. The elution will then be transferred to a clean PCR strip, before 5\u00b5L gets transferred to two tubes containing the reaction mix.\nThis concludes the OT-2 portion of the protocol and the user will be prompted to move the samples to 65c for a 20 minute incubation to complete the protocol. \nAdjust the parameters and download the protocol below. \nNote: This protocol is still a work in progress and will likely need further optimizations; please keep this in mind when using this protocol. \n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nP20 Single-Channel Pipette (left mount)\nP300 or P1000 Single-Channel Pipette (right mount)\nOpentrons 20\u00b5L Filter Tips\nOpentrons Filters Tips for P300 or P1000\nOpentrons Magnetic Module, GEN2\nOpentrons Temperature Module, GEN2\nOpentrons 4-in-1 Tube Rack\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nNEST 96-Deepwell Plate, 2mL\nNEST 1.5mL Centrifuge Tubes\nPCR Strips\nReagents\nSamples\n\n\n\nDeck Layout \nSlot 1: Opentrons 96-Well Aluminum Block with PCR Strips\nA1: Magnetic Beads\nB1: DNA\nColumns 2-4: Elution Destination (empty to begin)\nColumns 7-12: Reaction Mix + Elution Destination (empty to begin) \nSlot 2: Opentrons 20\u00b5L Filter Tips \nSlot 3: Opentrons Filters Tips for P300 or P1000 (Tiprack 3) \nSlot 4: Opentrons 4-in-1 Tube Rack with NEST 1.5mL Centrifuge Tubes\nNote: At the beginning of the protocol, samples should be loaded in the tube rack. Once transferred:\nA1: Buffer 3\nA4: Reaction Mix \nSlot 5: Opentrons 20\u00b5L Filter Tips \nSlot 6: Opentrons Filters Tips for P300 or P1000 (Tiprack 2) \nSlot 7: Opentrons Temperature Module, GEN2 with [Opentrons 24-Well Aluminum Block]((https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set) containing NEST 1.5mL Centrifuge Tubes \nSlot 8: NEST 12-Well Reservoir, 15mL\nA1: Buffer 1\nA2: Buffer 2 (Wash 1, Samples 1-12)\nA3: Buffer 2 (Wash 1, Samples 13-24)\nA4: Buffer 2 (Wash 2, Samples 1-12)\nA5: Buffer 2 (Wash 2, Samples 13-24)\nA6: Buffer 2 (Wash 3, Samples 1-12)\nA7: Buffer 2 (Wash 3, Samples 13-24) \nSlot 9: Opentrons Filters Tips for P300 or P1000 (Tiprack 1) \nSlot 10: Opentrons Magnetic Module, GEN2 with NEST 96-Deepwell Plate, 2mL \nSlot 11: NEST 1-Well Reservoir, 195mL (for liquid waste) \nUsing the customizations field (below), set up your protocol.\n Pipette & Tip Combo: Select which pipette (right mount) and corresponding tips are being used in this protocol.\n Number of Samples (1-24): Specify the number of samples to run (1-24).", "internal": "1eeb01", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", diff --git a/protoBuilds/1ef67e/README.json b/protoBuilds/1ef67e/README.json index aa724b3d0..66e511115 100644 --- a/protoBuilds/1ef67e/README.json +++ b/protoBuilds/1ef67e/README.json @@ -5,7 +5,7 @@ "Assay" ] }, - "description": "This protocol represents one of several protocols that prepares a panel of set dilutions of primary antibodies and fluorophores. This protocol creates Panel 1. The following antibodies and fluorophores dilutions are prepared in this panel:\nAntibodies\n* CD4\n* CD8\n* FOXP3\n* PD-L1 EL13N\n* PAN CK\n* KI-67\nFluorophores\n* 520\n* 570\n* 540\n* 620\n* 650\n* 690\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Single-Channel Pipette\nOpentrons P1000 Single-Channel Pipette\nOpentrons 10\u00b5L Tips\nOpentrons 1000\u00b5L Tips\nCustom Tube Holder for 6mL Tubes and Tubes\nBio-Rad 96 Well Plate\nOpentrons 4-in-1 Tube Rack\nOpentrons 4-in-1 Tube Rack\n50mL Tubes\n2mL Tubes\n15mL Tubes\nAntibodies\nFluorophores\n\n\n\nSlot 1: Opentrons 1000\u00b5L Tips\nSlot 2: Custom 6mL Tube Rack Holder and Tubes\nSlot 3: Bio-Rad 96 Well Plate, for sample aliquots\nSlot 4: Opentrons 10\u00b5L Tips\nSlot 5: Opentrons 4-in-1 Tube Rack; 6x15mL, 4x50mL\n* A3: Antibody Dilutent (initial volume=50mL)\n* A4: Fluorophore Dilutent (initial volume=50mL)\nSlot 6: Opentrons 4-in-1 Tube Rack; 24x2mL\nSetup with initial volumes\n* A1: 520, 75\u00b5L\n* B1: 540, 75\u00b5L\n* C1: 570, 75\u00b5L\n* D1: 620, 75\u00b5L\n* A2: 650, 75\u00b5L\n* B2: 690, 75\u00b5L\n* A3: CD3, 1000\u00b5L\n* B3: CD4, 100\u00b5L\n* C3: CD8, 100\u00b5L\n* D3: CD20, 250\u00b5L\n* A4: CD56, 1000\u00b5L\n* B4: CD68, 100\u00b5L\n* C4: CD163, 100\u00b5L\n* D4: PD1, 100\u00b5L\n* A5: PD-L1 EL13N, 100\u00b5L\n* B5: FOXP3, 500\u00b5L\n* C5: PAN CK, 1000\u00b5L\n* D5: KI-67, 2000\u00b5L (Source 1)\n* A6: KI-67, 2000\u00b5L (Source 2)\n* B6: KI-67, 2000\u00b5L (Source 3)\n* C6: KI-67, 2000\u00b5L (Source 4)\n* D6: KI-67, 2000\u00b5L (Source 5)", + "description": "This protocol represents one of several protocols that prepares a panel of set dilutions of primary antibodies and fluorophores. This protocol creates Panel 1. The following antibodies and fluorophores dilutions are prepared in this panel:\nAntibodies\n CD4\n CD8\n FOXP3\n PD-L1 EL13N\n PAN CK\n KI-67\nFluorophores\n 520\n 570\n 540\n 620\n 650\n 690\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Single-Channel Pipette\nOpentrons P1000 Single-Channel Pipette\nOpentrons 10\u00b5L Tips\nOpentrons 1000\u00b5L Tips\nCustom Tube Holder for 6mL Tubes and Tubes\nBio-Rad 96 Well Plate\nOpentrons 4-in-1 Tube Rack\nOpentrons 4-in-1 Tube Rack\n50mL Tubes\n2mL Tubes\n15mL Tubes\nAntibodies\nFluorophores\n\n\n\nSlot 1: Opentrons 1000\u00b5L Tips\nSlot 2: Custom 6mL Tube Rack Holder and Tubes\nSlot 3: Bio-Rad 96 Well Plate, for sample aliquots\nSlot 4: Opentrons 10\u00b5L Tips\nSlot 5: Opentrons 4-in-1 Tube Rack; 6x15mL, 4x50mL\n A3: Antibody Dilutent (initial volume=50mL)\n A4: Fluorophore Dilutent (initial volume=50mL)\nSlot 6: Opentrons 4-in-1 Tube Rack; 24x2mL\nSetup with initial volumes\n A1: 520, 75\u00b5L\n B1: 540, 75\u00b5L\n C1: 570, 75\u00b5L\n D1: 620, 75\u00b5L\n A2: 650, 75\u00b5L\n B2: 690, 75\u00b5L\n A3: CD3, 1000\u00b5L\n B3: CD4, 100\u00b5L\n C3: CD8, 100\u00b5L\n D3: CD20, 250\u00b5L\n A4: CD56, 1000\u00b5L\n B4: CD68, 100\u00b5L\n C4: CD163, 100\u00b5L\n D4: PD1, 100\u00b5L\n A5: PD-L1 EL13N, 100\u00b5L\n B5: FOXP3, 500\u00b5L\n C5: PAN CK, 1000\u00b5L\n D5: KI-67, 2000\u00b5L (Source 1)\n A6: KI-67, 2000\u00b5L (Source 2)\n B6: KI-67, 2000\u00b5L (Source 3)\n C6: KI-67, 2000\u00b5L (Source 4)\n D6: KI-67, 2000\u00b5L (Source 5)", "internal": "1ef67e", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1f62ba/README.json b/protoBuilds/1f62ba/README.json index 9f2a8e263..8f26f32b4 100644 --- a/protoBuilds/1f62ba/README.json +++ b/protoBuilds/1f62ba/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps one PCR plate with DNA, water, primer letter, primer number, and Kappa enzyme. New tips are granted for DNA and primers, whereas just one column of tips is used for the Kappa enzyme and water, respectively. The water is added via multi-dispensing.\nExplanation of complex parameters below:\n* Number of Columns: Specify the number of DNA columns for this protocol.\n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n", + "description": "This protocol preps one PCR plate with DNA, water, primer letter, primer number, and Kappa enzyme. New tips are granted for DNA and primers, whereas just one column of tips is used for the Kappa enzyme and water, respectively. The water is added via multi-dispensing.\nExplanation of complex parameters below:\n Number of Columns: Specify the number of DNA columns for this protocol.\n P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n", "internal": "1f62ba", "labware": "\nNest 12-well reservoir, 15mL\n20ul Filter Tips\n", "markdown": { diff --git a/protoBuilds/1f96ca-part-2/README.json b/protoBuilds/1f96ca-part-2/README.json index e8be0bd87..77356257d 100644 --- a/protoBuilds/1f96ca-part-2/README.json +++ b/protoBuilds/1f96ca-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Magnetic Module (Deck Slot 9)\nOpentrons p300 tips (Deck Slots 10, 11)\nOpentrons p20 tips (Deck Slots 3, 4, 7, 8)\nopentrons_96_aluminumblock_generic_pcr_strip_200ul (Deck Slot 5) with\nbeads, water, intermediate_pools in columns 1-3\npost-PCR plate (Deck Slot 1)\nnest_12_reservoir_15ml (Deck Slot 2)\npool tube and tube rack (Deck Slot 6) with pool tube in A1\n", - "description": "Part 2 of 2: Library Clean Up and Pooling\nLinks:\n* Part 1: Fragmentation, End Repair, Adapter Ligation, Library Amplification\n* Part 2: Clean Up Libraries\nWith this protocol, your robot can perform the ROCHE KAPA HyperPlus NGS library prep protocol described by the KAPA HyperPlus Kit.\nThis is part 2 of the protocol, which includes the steps (1) bead clean up (2) pooling.", + "description": "Part 2 of 2: Library Clean Up and Pooling\nLinks:\n Part 1: Fragmentation, End Repair, Adapter Ligation, Library Amplification\n Part 2: Clean Up Libraries\nWith this protocol, your robot can perform the ROCHE KAPA HyperPlus NGS library prep protocol described by the KAPA HyperPlus Kit.\nThis is part 2 of the protocol, which includes the steps (1) bead clean up (2) pooling.", "internal": "1f96ca", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1f96ca/README.json b/protoBuilds/1f96ca/README.json index 44622c4fa..b8d6bfe49 100644 --- a/protoBuilds/1f96ca/README.json +++ b/protoBuilds/1f96ca/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Thermocycler Module (Deck Slots 7, 8, 10, 11)\nOpentrons Magnetic Module (Deck Slot 9)\nOpentrons p300 tips (Deck Slot 4)\nOpentrons p20 tips (Deck Slots 3, 6)\nopentrons_96_aluminumblock_generic_pcr_strip_200ul (Deck Slot 5) with\nfrag_mm, erat_mm, liga_mm, beads, water, kapa mix in columns 1-6\nDNA sample plate (Deck Slot 1)\nnest_12_reservoir_15ml (Deck Slot 2)\n", - "description": "Part 1 of 2: Fragmentation, End Repair, Adapter Ligation, Library Amplification\nLinks:\n* Part 1: Fragmentation, End Repair, Adapter Ligation, Library Amplification\n* Part 2: Clean Up Libraries\nWith this protocol, your robot can perform the ROCHE KAPA HyperPlus NGS library prep protocol described by the KAPA HyperPlus Kit.\nThis is part 1 of the protocol, which includes the steps (1) enzymatic DNA fragmentation (2) end repair and A-tailing (3) adapter ligation and (4) library amplification.\nThe double stranded DNA fragments are end-repaired to generate 5'-phosphorylated, 3'-dA-tailed dsDNA. dsDNA adapters with 3'-dTMP overhangs are ligated to the 3'-dA-tailed DNA. These steps are followed by PCR amplification of the libraries.", + "description": "Part 1 of 2: Fragmentation, End Repair, Adapter Ligation, Library Amplification\nLinks:\n Part 1: Fragmentation, End Repair, Adapter Ligation, Library Amplification\n Part 2: Clean Up Libraries\nWith this protocol, your robot can perform the ROCHE KAPA HyperPlus NGS library prep protocol described by the KAPA HyperPlus Kit.\nThis is part 1 of the protocol, which includes the steps (1) enzymatic DNA fragmentation (2) end repair and A-tailing (3) adapter ligation and (4) library amplification.\nThe double stranded DNA fragments are end-repaired to generate 5'-phosphorylated, 3'-dA-tailed dsDNA. dsDNA adapters with 3'-dTMP overhangs are ligated to the 3'-dA-tailed DNA. These steps are followed by PCR amplification of the libraries.", "internal": "1f96ca", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/1fcf02/README.json b/protoBuilds/1fcf02/README.json index d0627e0c4..41df82e5a 100644 --- a/protoBuilds/1fcf02/README.json +++ b/protoBuilds/1fcf02/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps (3) 384 plates with urea, buffer and sample. One tip is used for each the urea and buffer reagents, with changing tips for the sample. Pipettes are selected dependent on the volume passed to the csv. If the protocol runs out of tips, it will pause and prompt the user to refill tip racks and resume. After sample is added, the well is mixed at 20ul for 3 repetitions.\nExplanation of complex parameters below:\n* Number of 384 plates: Specify how many 384 well plates there are for this run. Note that for plates less than 3, plates should be placed in order of slot number (1, 2, then 3), and csvs should also be uploaded in that order (from the top down below).\n* .CSV: Find below the format for the urea/buffer, and sample csvs. NOTE: Always put an \"x\" in the top left well of the csv, and include the header line. All csvs should be seperate. For wells which receive no volume, input an \"x\" instead. Please see the csvs below for reference.\n\nUrea/buffer map:\n\n\nSample map:\n\n\n\nUrea/Buffer Initial Volume (mL): Specify the initial volume in mL in each the urea and buffer tubes.\n\nP20/P300 Mount: Specify which mount (left or right) to host the single-channel pipettes.\n\n", + "description": "This protocol preps (3) 384 plates with urea, buffer and sample. One tip is used for each the urea and buffer reagents, with changing tips for the sample. Pipettes are selected dependent on the volume passed to the csv. If the protocol runs out of tips, it will pause and prompt the user to refill tip racks and resume. After sample is added, the well is mixed at 20ul for 3 repetitions.\nExplanation of complex parameters below:\n Number of 384 plates: Specify how many 384 well plates there are for this run. Note that for plates less than 3, plates should be placed in order of slot number (1, 2, then 3), and csvs should also be uploaded in that order (from the top down below).\n .CSV: Find below the format for the urea/buffer, and sample csvs. NOTE: Always put an \"x\" in the top left well of the csv, and include the header line. All csvs should be seperate. For wells which receive no volume, input an \"x\" instead. Please see the csvs below for reference.\n\nUrea/buffer map:\n\n\nSample map:\n\n\n\nUrea/Buffer Initial Volume (mL): Specify the initial volume in mL in each the urea and buffer tubes.\n\nP20/P300 Mount: Specify which mount (left or right) to host the single-channel pipettes.\n\n", "internal": "1fcf02", "labware": "\nOpentrons 4-in-1 Tube Rack\nGreiner 384 Well Plate\nOpentrons 20ul Tips\nOpentrons 300ul Tips\n", "markdown": { diff --git a/protoBuilds/203136/README.json b/protoBuilds/203136/README.json index 56eec2874..9e3e84940 100644 --- a/protoBuilds/203136/README.json +++ b/protoBuilds/203136/README.json @@ -5,7 +5,7 @@ "Invitrogen ChargeSwitch" ] }, - "description": "This protocol performs the Invitrogen ChargeSwitch gDNA Kit, using the P50 Single-Channel Pipette and the P300 Multi-Channel Pipette.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P50 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nBio-Rad 96-Well Plate, 200\u00b5L\nUSA Scientific 96-Deep Well Plate, 2.4mL\nUSA Scientific 12-Well Reservoir, 22mL\nReagents\nSamples\n\n\n\nSlot 1: Bio-Rad 96-Well Plate, clean and empty (for final elution)\nSlot 2: Opentrons 50/300\u00b5L Tips\nSlot 3: Opentrons 50/300\u00b5L Tips\nSlot 4: Opentrons Magnetic Module with a 96-Deep Well Plate, filled with 200\u00b5L of sample\nSlot 5: Opentrons 50/300\u00b5L Tips\nSlot 6: Opentrons 50/300\u00b5L Tips\nSlot 7: USA Scientific 12-Well Reservoir\n* A1: Lysis Buffer\n* A2: Proteinase K\n* A3: Purification Buffer\n* A4: Mag Beads\n* A5: Wash Buffer (Wash 1)\n* A6: Wash Buffer (Wash 2)\n* A7: Elution Buffer\n* A8: Empty, for liquid waste\n* A9: Empty, for liquid waste\n* A10: Empty, for liquid waste\n* A11: Empty, for liquid waste\n* A12: Empty, for liquid waste\nSlot 8: Opentrons 50/300\u00b5L Tips\nSlot 9: Opentrons 50/300\u00b5L Tips\nSlot 10: Opentrons 50/300\u00b5L Tips\nSlot 11: Opentrons 50/300\u00b5L Tips\nUsing the customizations fields, below set up your protocol.\n* P300 Multi Mount: Select which mount (left or right) the P300 Multi is attached to.\n* P50 Single Mount: Select which mount (left or right) the P50 Single is attached to.\n* Number of Samples: Specify the number of samples you'd like to run.\nNote: The number of tips needed, will change according to the number of samples you select. For example, if running 96 samples, you'd need 8 tip racks, but if running 8 samples, only 1 tip rack is required. When you upload the protocol, you should see an updated deck layout with the necessary tip racks shown.", + "description": "This protocol performs the Invitrogen ChargeSwitch gDNA Kit, using the P50 Single-Channel Pipette and the P300 Multi-Channel Pipette.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P50 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nBio-Rad 96-Well Plate, 200\u00b5L\nUSA Scientific 96-Deep Well Plate, 2.4mL\nUSA Scientific 12-Well Reservoir, 22mL\nReagents\nSamples\n\n\n\nSlot 1: Bio-Rad 96-Well Plate, clean and empty (for final elution)\nSlot 2: Opentrons 50/300\u00b5L Tips\nSlot 3: Opentrons 50/300\u00b5L Tips\nSlot 4: Opentrons Magnetic Module with a 96-Deep Well Plate, filled with 200\u00b5L of sample\nSlot 5: Opentrons 50/300\u00b5L Tips\nSlot 6: Opentrons 50/300\u00b5L Tips\nSlot 7: USA Scientific 12-Well Reservoir\n A1: Lysis Buffer\n A2: Proteinase K\n A3: Purification Buffer\n A4: Mag Beads\n A5: Wash Buffer (Wash 1)\n A6: Wash Buffer (Wash 2)\n A7: Elution Buffer\n A8: Empty, for liquid waste\n A9: Empty, for liquid waste\n A10: Empty, for liquid waste\n A11: Empty, for liquid waste\n A12: Empty, for liquid waste\nSlot 8: Opentrons 50/300\u00b5L Tips\nSlot 9: Opentrons 50/300\u00b5L Tips\nSlot 10: Opentrons 50/300\u00b5L Tips\nSlot 11: Opentrons 50/300\u00b5L Tips\nUsing the customizations fields, below set up your protocol.\n P300 Multi Mount: Select which mount (left or right) the P300 Multi is attached to.\n P50 Single Mount: Select which mount (left or right) the P50 Single is attached to.\n* Number of Samples: Specify the number of samples you'd like to run.\nNote: The number of tips needed, will change according to the number of samples you select. For example, if running 96 samples, you'd need 8 tip racks, but if running 8 samples, only 1 tip rack is required. When you upload the protocol, you should see an updated deck layout with the necessary tip racks shown.", "internal": "203136", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/2082dd/README.json b/protoBuilds/2082dd/README.json index e60c39c51..a38132b14 100644 --- a/protoBuilds/2082dd/README.json +++ b/protoBuilds/2082dd/README.json @@ -5,7 +5,7 @@ "Cherrypicking" ] }, - "description": "This protocol performs a NGS library prep through 2 fold dilutions and final pooling. All volumes are specified in a .csv file.\n\n\n\nBio-Rad Hardshell 96-well PCR plate 200ul #HSP9601\nOpentrons 4-in-1 tuberack with 4x6 insert\nOpentrons 4-in-1 tuberack with 3x5 insert holding 15ml NEST centrifuge tubes or equivalent\nOpentrons P20 and P300 GEN2 single-channel electronic pipettes\nOpentrons 20ul and 300ul tipracks\n\n\n\n3x5 tuberack (slot 4)\n* tube A1: TE buffer (filled to at least ~3cm below tube opening)\n4x6 tuberack (slot 5)\n* tubes A1: 1.5ml snapcap tube for pooling\n* tube A2: 1.5ml screwcap tube for final pooled libraries", + "description": "This protocol performs a NGS library prep through 2 fold dilutions and final pooling. All volumes are specified in a .csv file.\n\n\n\nBio-Rad Hardshell 96-well PCR plate 200ul #HSP9601\nOpentrons 4-in-1 tuberack with 4x6 insert\nOpentrons 4-in-1 tuberack with 3x5 insert holding 15ml NEST centrifuge tubes or equivalent\nOpentrons P20 and P300 GEN2 single-channel electronic pipettes\nOpentrons 20ul and 300ul tipracks\n\n\n\n3x5 tuberack (slot 4)\n* tube A1: TE buffer (filled to at least ~3cm below tube opening)\n4x6 tuberack (slot 5)\n tubes A1: 1.5ml snapcap tube for pooling\n tube A2: 1.5ml screwcap tube for final pooled libraries", "internal": "2082dd", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/211a24/README.json b/protoBuilds/211a24/README.json index ca1422abd..97bd4e7a8 100644 --- a/protoBuilds/211a24/README.json +++ b/protoBuilds/211a24/README.json @@ -5,7 +5,7 @@ "Serial Dilution" ] }, - "description": "This protocol allows for a customizable serial dilution workflow based on 4 text files containing worklist information. This protocol uses a P300 GEN2 single-channel pipette. The 4 steps, each corresponding to its own input text file, are as follows:\n* diluent addition to serial dilution plate\n* sample addition to serial dilution plate\n* serial dilution across plate\n* cherrypicking to load final plate", + "description": "This protocol allows for a customizable serial dilution workflow based on 4 text files containing worklist information. This protocol uses a P300 GEN2 single-channel pipette. The 4 steps, each corresponding to its own input text file, are as follows:\n diluent addition to serial dilution plate\n sample addition to serial dilution plate\n serial dilution across plate\n cherrypicking to load final plate", "internal": "211a24", "labware": "\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nNEST 1 Well Reservoir 195 mL\nOpentrons 96 Tip Rack 300 \u00b5L\n", "markdown": { diff --git a/protoBuilds/211fe1/README.json b/protoBuilds/211fe1/README.json index 02b2d07aa..e70a0907f 100644 --- a/protoBuilds/211fe1/README.json +++ b/protoBuilds/211fe1/README.json @@ -5,7 +5,7 @@ "Mass Spec" ] }, - "description": "This protocol performs mass spec sample prep on up to 96 samples using an Opentrons thermocycler for incubation steps. Samples should be specified as comma-separated values on the first line of a .csv file, as in the following example:\nA1,B1,C1,D1,E1,G1,B2\nThe samples are filled according to the order of the .csv, and invalid wells are ignored (valid wells must be A1-H12)\n\n\n\nNEST 96-well PCR plate 100\u00b5L #402501 mounted in Opentrons Thermocycler\nNEST 1.5ml snapcap microcentrifuge tubes (or equivalent) mounted in Opentrons 4-in-1 tuberack with 4x6 insert\nOpentrons P20 GEN2 electronic pipette\nOpentrons 10/20ul tiprack\n\n\n\nOpentrons 4-in-1 tuberack with 4x6 1.5ml tube insert\n* tube A1: enzyme\n* tube B1: reagent 1\n* tube C1: reagent 2", + "description": "This protocol performs mass spec sample prep on up to 96 samples using an Opentrons thermocycler for incubation steps. Samples should be specified as comma-separated values on the first line of a .csv file, as in the following example:\nA1,B1,C1,D1,E1,G1,B2\nThe samples are filled according to the order of the .csv, and invalid wells are ignored (valid wells must be A1-H12)\n\n\n\nNEST 96-well PCR plate 100\u00b5L #402501 mounted in Opentrons Thermocycler\nNEST 1.5ml snapcap microcentrifuge tubes (or equivalent) mounted in Opentrons 4-in-1 tuberack with 4x6 insert\nOpentrons P20 GEN2 electronic pipette\nOpentrons 10/20ul tiprack\n\n\n\nOpentrons 4-in-1 tuberack with 4x6 1.5ml tube insert\n tube A1: enzyme\n tube B1: reagent 1\n* tube C1: reagent 2", "internal": "211fe1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/21e4d8-pt1/README.json b/protoBuilds/21e4d8-pt1/README.json index 925fa7ee8..a8373fe18 100644 --- a/protoBuilds/21e4d8-pt1/README.json +++ b/protoBuilds/21e4d8-pt1/README.json @@ -5,7 +5,7 @@ "Twist Library Prep" ] }, - "description": "This protocol is part one of a three-part series to automate the Twist Library Prep protocol. See below for all three parts:\n\nPart 1: Fragmentation & Repair\nPart 2: Ligate Adapters\nPart 3: PCR Amplification\n\nThis protocol begins with samples diluted to 5ng/\u00b5L (if you still need to normalize your sample concentration, try our Normalization protocol) in either PCR tubes or a 96-well plate. Enzymatic Fragmentation Mastermix (40\u00b5L) is added to empty PCR tubes/96-well plate first, before 10\u00b5L of normalized sample is added. The PCR tubes/96-well plate containing sample and mastermix should then be moved off deck to thermocycler and run on the program listed in the Twist Library Prep protocol. After the thermocycler, the samples can be returned to the OT-2 for part two of this protocol.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 (Single- or Multi-Channel) Pipette\nOpentrons p300 (Single- or Multi-Channel) Pipette\nOpentrons Tips\noptional: Opentrons Thermocycler or Opentrons Temperature Module, for active cooling during protocol\nNEST 96-Well PCR Plate\nOpentrons Tube Rack or Aluminum Block Set\nMicrocentrifuge Tube, 1.5mL or PCR strips\nSamples\nTwist Enzymatic Fragmentation and Twist Universal Adapter System\n\n\n\nDeck Layout\n\nSlot 1: Normalized samples in NEST 96-Well PCR Plate or PCR tubes on 96-Well Aluminum Block\n\nSlot 2 (if using P300 Single-Channel): Enyzmatic Fragmentation Master Mix in Microcentrifuge Tube, 1.5mL in Opentrons Tube Rack or 24-Well Aluminum Block\nTubes should be loaded in A1, A2, and A3; each tube can accommodate up to 32 samples and will be used sequentially\nSlot 2 (if using P300 Multi-Channel): Enyzmatic Fragmentation Master Mix in NEST 96-Well PCR Plate or PCR tubes on 96-Well Aluminum Block\nColumns 1, 2, and 3 should be loaded; each column can accommodate up to 32 samples and will be used sequentially\n\nSlot 3: Opentrons Tips for P300\n\nSlot 6: Opentrons Tips for P20\n\nSlot 7: NEST 96-Well PCR Plate or PCR tubes on 96-Well Aluminum Block with optional Opentrons Thermocycler or Opentrons Temperature Module, for active cooling during protocol\n\nUsing the customizations field (below), set up your protocol.\n* P20 Type: Select the type (Single- or Multi-Channel) to use; P20 should should be mounted on the left mount\n* P300 Type: Select the type (Single- or Multi-Channel) to use; P300 should should be mounted on the right mount\n* Number of Samples: Specify the number of samples to run (1-96).\n* Module (for cooling): Select whether or not an Opentrons module will be used for active cooling during protocol\n* Destination Plate: Select the labware that will be used to combine the samples and the master mix\n* Sample Plate: Select the labware that will contain the gDNA samples\n* Master Mix Labware: Select the labware that will contain the enzymatic fragmentation master mix\n\n", + "description": "This protocol is part one of a three-part series to automate the Twist Library Prep protocol. See below for all three parts:\n\nPart 1: Fragmentation & Repair\nPart 2: Ligate Adapters\nPart 3: PCR Amplification\n\nThis protocol begins with samples diluted to 5ng/\u00b5L (if you still need to normalize your sample concentration, try our Normalization protocol) in either PCR tubes or a 96-well plate. Enzymatic Fragmentation Mastermix (40\u00b5L) is added to empty PCR tubes/96-well plate first, before 10\u00b5L of normalized sample is added. The PCR tubes/96-well plate containing sample and mastermix should then be moved off deck to thermocycler and run on the program listed in the Twist Library Prep protocol. After the thermocycler, the samples can be returned to the OT-2 for part two of this protocol.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 (Single- or Multi-Channel) Pipette\nOpentrons p300 (Single- or Multi-Channel) Pipette\nOpentrons Tips\noptional: Opentrons Thermocycler or Opentrons Temperature Module, for active cooling during protocol\nNEST 96-Well PCR Plate\nOpentrons Tube Rack or Aluminum Block Set\nMicrocentrifuge Tube, 1.5mL or PCR strips\nSamples\nTwist Enzymatic Fragmentation and Twist Universal Adapter System\n\n\n\nDeck Layout\n\nSlot 1: Normalized samples in NEST 96-Well PCR Plate or PCR tubes on 96-Well Aluminum Block\n\nSlot 2 (if using P300 Single-Channel): Enyzmatic Fragmentation Master Mix in Microcentrifuge Tube, 1.5mL in Opentrons Tube Rack or 24-Well Aluminum Block\nTubes should be loaded in A1, A2, and A3; each tube can accommodate up to 32 samples and will be used sequentially\nSlot 2 (if using P300 Multi-Channel): Enyzmatic Fragmentation Master Mix in NEST 96-Well PCR Plate or PCR tubes on 96-Well Aluminum Block\nColumns 1, 2, and 3 should be loaded; each column can accommodate up to 32 samples and will be used sequentially\n\nSlot 3: Opentrons Tips for P300\n\nSlot 6: Opentrons Tips for P20\n\nSlot 7: NEST 96-Well PCR Plate or PCR tubes on 96-Well Aluminum Block with optional Opentrons Thermocycler or Opentrons Temperature Module, for active cooling during protocol\n\nUsing the customizations field (below), set up your protocol.\n P20 Type: Select the type (Single- or Multi-Channel) to use; P20 should should be mounted on the left mount\n P300 Type: Select the type (Single- or Multi-Channel) to use; P300 should should be mounted on the right mount\n Number of Samples: Specify the number of samples to run (1-96).\n Module (for cooling): Select whether or not an Opentrons module will be used for active cooling during protocol\n Destination Plate: Select the labware that will be used to combine the samples and the master mix\n Sample Plate: Select the labware that will contain the gDNA samples\n* Master Mix Labware: Select the labware that will contain the enzymatic fragmentation master mix\n\n", "internal": "21e4d8-pt1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/21e4d8-pt2/README.json b/protoBuilds/21e4d8-pt2/README.json index 883fd3371..cf3c1902d 100644 --- a/protoBuilds/21e4d8-pt2/README.json +++ b/protoBuilds/21e4d8-pt2/README.json @@ -5,7 +5,7 @@ "Twist Library Prep" ] }, - "description": "This protocol is part two of a three-part series to automate the Twist Library Prep protocol. See below for all three parts:\n\nPart 1: Fragmentation & Repair\nPart 2: Ligate Adapters\nPart 3: PCR Amplification\n\nThe final plate from part one should be run through the thermocycler program outlined in the Twist Library Prep protocol before being moved back to the OT-2 for this protocol.\n\nThis protocol begins by adding 5\u00b5L of the Twist Universal Adapters to each well containing samples from part one, followed by the addition of 45\u00b5L of Ligation Master Mix. The user is then prompted to remove plate and incubate the samples on a thermocycler. Following incubation, the user will return the plate to the OT-2 for a fully-automated magbead-based wash process (2 times) that will result in the 15\u00b5L of supernatant transferred to labware selected by the user. The user should then take the labware containing the supernatant and run on the thermocycler before moving to part three.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 (Single- or Multi-Channel) Pipette\nOpentrons p300 (Single- or Multi-Channel) Pipette\nOpentrons Tips\nOpentrons Magnetic Module\nOptional, Opentrons Temperature Module, for active cooling during protocol\nMulti-Well Reservoir, such as the NEST 12-Well Reservoir or USA Scientific 12-Well Reservoir\nNEST 96-Well PCR Plate\nOpentrons Tube Rack or Aluminum Block Set\nMicrocentrifuge Tube, 1.5mL or PCR strips\nSamples\nTwist Enzymatic Fragmentation and Twist Universal Adapter System\nOptional, Single-Well Reservoir, such as the NEST 1-Well Reservoir, 195mL or Agilent 1-Well Reservoir, 290mL, for liquid waste\n\n\n\nDeck Layout\n\nSlot 1: Empty Destination PCR Labware (such as NEST 96-Well PCR Plate or PCR Strips in 96-Well Aluminum Block)\n\nSlot 2: Plate containing Twist Universal Adapters\n\nSlot 3: Opentrons Tips for P300\n\nSlot 4: Multi-Well Reservoir\nLayout for 12-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 1, samples 1-48 (200\u00b5L per sample)\nA4: Freshly prepared 80% ethanol for wash 1, samples 48-96 (200\u00b5L per sample)\nA5: Freshly prepared 80% ethanol for wash 2, samples 1-48 (200\u00b5L per sample)\nA6: Freshly prepared 80% ethanol for wash 2, samples 48-96 (200\u00b5L per sample)\nA12: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\nLayout for 4-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA2: Freshly prepared 80% ethanol for wash 1, samples 1-96 (200\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 2, samples 1-96 (200\u00b5L per sample)\nA4: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\n\nSlot 5: Opentrons Tips for P20\n\nSlot 6: Opentrons Tips for P300\n\nSlot 7: Labware containing ligation master mix (on Opentrons Temperature Module, if active cooling during protocol)\n\nSlot 10: Opentrons Magnetic Module with plate from part one\n\nOptional, Slot 11: Single-Well Reservoir for liquid waste\n\nUsing the customizations field (below), set up your protocol.\n* P20 Type: Select the type (Single- or Multi-Channel) to use; P20 should should be mounted on the left mount\n* P300 Type: Select the type (Single- or Multi-Channel) to use; P300 should should be mounted on the right mount\n* Number of Samples: Specify the number of samples to run (1-96)\n* Type of MagDeck: Select which generation (1, 2) magnetic module to use\n* Plate on MagDeck: Select which labware type contains samples and is placed on magnetic module\n* Module (for cooling): Select whether or not an Opentrons module will be used for active cooling during protocol\n* Destination Plate: Select the labware that will be used for the elutions\n* Reservor for Reagents: Select which reservoir will be used for reagents\n* Sample Plate: Select the labware that will contain the gDNA samples\n* Master Mix Labware: Select the labware that will contain the ligation master mix\n* Liquid Waste Destination: Select where liquid waste should be disposed of\n\n", + "description": "This protocol is part two of a three-part series to automate the Twist Library Prep protocol. See below for all three parts:\n\nPart 1: Fragmentation & Repair\nPart 2: Ligate Adapters\nPart 3: PCR Amplification\n\nThe final plate from part one should be run through the thermocycler program outlined in the Twist Library Prep protocol before being moved back to the OT-2 for this protocol.\n\nThis protocol begins by adding 5\u00b5L of the Twist Universal Adapters to each well containing samples from part one, followed by the addition of 45\u00b5L of Ligation Master Mix. The user is then prompted to remove plate and incubate the samples on a thermocycler. Following incubation, the user will return the plate to the OT-2 for a fully-automated magbead-based wash process (2 times) that will result in the 15\u00b5L of supernatant transferred to labware selected by the user. The user should then take the labware containing the supernatant and run on the thermocycler before moving to part three.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 (Single- or Multi-Channel) Pipette\nOpentrons p300 (Single- or Multi-Channel) Pipette\nOpentrons Tips\nOpentrons Magnetic Module\nOptional, Opentrons Temperature Module, for active cooling during protocol\nMulti-Well Reservoir, such as the NEST 12-Well Reservoir or USA Scientific 12-Well Reservoir\nNEST 96-Well PCR Plate\nOpentrons Tube Rack or Aluminum Block Set\nMicrocentrifuge Tube, 1.5mL or PCR strips\nSamples\nTwist Enzymatic Fragmentation and Twist Universal Adapter System\nOptional, Single-Well Reservoir, such as the NEST 1-Well Reservoir, 195mL or Agilent 1-Well Reservoir, 290mL, for liquid waste\n\n\n\nDeck Layout\n\nSlot 1: Empty Destination PCR Labware (such as NEST 96-Well PCR Plate or PCR Strips in 96-Well Aluminum Block)\n\nSlot 2: Plate containing Twist Universal Adapters\n\nSlot 3: Opentrons Tips for P300\n\nSlot 4: Multi-Well Reservoir\nLayout for 12-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 1, samples 1-48 (200\u00b5L per sample)\nA4: Freshly prepared 80% ethanol for wash 1, samples 48-96 (200\u00b5L per sample)\nA5: Freshly prepared 80% ethanol for wash 2, samples 1-48 (200\u00b5L per sample)\nA6: Freshly prepared 80% ethanol for wash 2, samples 48-96 (200\u00b5L per sample)\nA12: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\nLayout for 4-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA2: Freshly prepared 80% ethanol for wash 1, samples 1-96 (200\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 2, samples 1-96 (200\u00b5L per sample)\nA4: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\n\nSlot 5: Opentrons Tips for P20\n\nSlot 6: Opentrons Tips for P300\n\nSlot 7: Labware containing ligation master mix (on Opentrons Temperature Module, if active cooling during protocol)\n\nSlot 10: Opentrons Magnetic Module with plate from part one\n\nOptional, Slot 11: Single-Well Reservoir for liquid waste\n\nUsing the customizations field (below), set up your protocol.\n P20 Type: Select the type (Single- or Multi-Channel) to use; P20 should should be mounted on the left mount\n P300 Type: Select the type (Single- or Multi-Channel) to use; P300 should should be mounted on the right mount\n Number of Samples: Specify the number of samples to run (1-96)\n Type of MagDeck: Select which generation (1, 2) magnetic module to use\n Plate on MagDeck: Select which labware type contains samples and is placed on magnetic module\n Module (for cooling): Select whether or not an Opentrons module will be used for active cooling during protocol\n Destination Plate: Select the labware that will be used for the elutions\n Reservor for Reagents: Select which reservoir will be used for reagents\n Sample Plate: Select the labware that will contain the gDNA samples\n Master Mix Labware: Select the labware that will contain the ligation master mix\n* Liquid Waste Destination: Select where liquid waste should be disposed of\n\n", "internal": "21e4d8-pt2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/21e4d8-pt3/README.json b/protoBuilds/21e4d8-pt3/README.json index 7c6c15847..424d97e28 100644 --- a/protoBuilds/21e4d8-pt3/README.json +++ b/protoBuilds/21e4d8-pt3/README.json @@ -5,7 +5,7 @@ "Twist Library Prep" ] }, - "description": "This protocol is part three of a three-part series to automate the Twist Library Prep protocol. See below for all three parts:\n\nPart 1: Fragmentation & Repair\nPart 2: Ligate Adapters\nPart 3: PCR Amplification\n\nThe final plate from part two should be moved back to the OT-2 for this protocol.\n\nThis protocol begins by adding 10\u00b5L of the Twist UDI Primers to each well containing samples from part two, followed by the addition of 25\u00b5L of KAPA HiFi HotStart ReadyMix. The user is then prompted to remove plate and incubate the samples on a thermocycler. Following incubation, the user will return the plate to the OT-2 for a fully-automated magbead-based wash process (2 times) that will result in the 20\u00b5L of supernatant transferred to labware selected by the user. This completes the three-part Twist NGS Library Prep. The user can then perform QC or downstream applications on the elutes.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 (Single- or Multi-Channel) Pipette\nOpentrons p300 (Single- or Multi-Channel) Pipette\nOpentrons Tips\nOpentrons Magnetic Module\nOptional, Opentrons Temperature Module, for active cooling during protocol\nMulti-Well Reservoir, such as the NEST 12-Well Reservoir or USA Scientific 12-Well Reservoir\nNEST 96-Well PCR Plate\nOpentrons Tube Rack or Aluminum Block Set\nMicrocentrifuge Tube, 1.5mL or PCR strips\nSamples\nTwist Enzymatic Fragmentation and Twist Universal Adapter System\nOptional, Single-Well Reservoir, such as the NEST 1-Well Reservoir, 195mL or Agilent 1-Well Reservoir, 290mL, for liquid waste\n\n\n\nDeck Layout\n\nSlot 1: Empty Destination PCR Labware (such as NEST 96-Well PCR Plate or PCR Strips in 96-Well Aluminum Block)\n\nSlot 2: Opentrons Tips for P20\n\nSlot 3: Opentrons Tips for P300\n\nSlot 4: Plate containing Twist UDI Prmer (on Opentrons Temperature Module, if active cooling during protocol)\nSlot 5: Labware containing KAPA HiFi HotStart ReadyMix\n\nSlot 6: Opentrons Tips for P300\n\nSlot 8: Multi-Well Reservoir\nLayout for 12-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 1, samples 1-48 (200\u00b5L per sample)\nA4: Freshly prepared 80% ethanol for wash 1, samples 48-96 (200\u00b5L per sample)\nA5: Freshly prepared 80% ethanol for wash 2, samples 1-48 (200\u00b5L per sample)\nA6: Freshly prepared 80% ethanol for wash 2, samples 48-96 (200\u00b5L per sample)\nA12: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\nLayout for 4-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA2: Freshly prepared 80% ethanol for wash 1, samples 1-96 (200\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 2, samples 1-96 (200\u00b5L per sample)\nA4: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\n\nSlot 9: Opentrons Tips for P300\n\nSlot 10: Opentrons Magnetic Module with plate from part two\n\nOptional, Slot 11: Single-Well Reservoir for liquid waste\n\nUsing the customizations field (below), set up your protocol.\n* P20 Type: Select the type (Single- or Multi-Channel) to use; P20 should should be mounted on the left mount\n* P300 Type: Select the type (Single- or Multi-Channel) to use; P300 should should be mounted on the right mount\n* Number of Samples: Specify the number of samples to run (1-96)\n* Type of MagDeck: Select which generation (1, 2) magnetic module to use\n* Plate on MagDeck: Select which labware type contains samples and is placed on magnetic module\n* Module (for cooling): Select whether or not an Opentrons module will be used for active cooling during protocol\n* Destination Plate: Select the labware that will be used for the elutions\n* Reservor for Reagents: Select which reservoir will be used for reagents\n* Kapa Mix Labware: Select the labware that will contain the ligation master mix\n* Liquid Waste Destination: Select where liquid waste should be disposed of\n\n", + "description": "This protocol is part three of a three-part series to automate the Twist Library Prep protocol. See below for all three parts:\n\nPart 1: Fragmentation & Repair\nPart 2: Ligate Adapters\nPart 3: PCR Amplification\n\nThe final plate from part two should be moved back to the OT-2 for this protocol.\n\nThis protocol begins by adding 10\u00b5L of the Twist UDI Primers to each well containing samples from part two, followed by the addition of 25\u00b5L of KAPA HiFi HotStart ReadyMix. The user is then prompted to remove plate and incubate the samples on a thermocycler. Following incubation, the user will return the plate to the OT-2 for a fully-automated magbead-based wash process (2 times) that will result in the 20\u00b5L of supernatant transferred to labware selected by the user. This completes the three-part Twist NGS Library Prep. The user can then perform QC or downstream applications on the elutes.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 (Single- or Multi-Channel) Pipette\nOpentrons p300 (Single- or Multi-Channel) Pipette\nOpentrons Tips\nOpentrons Magnetic Module\nOptional, Opentrons Temperature Module, for active cooling during protocol\nMulti-Well Reservoir, such as the NEST 12-Well Reservoir or USA Scientific 12-Well Reservoir\nNEST 96-Well PCR Plate\nOpentrons Tube Rack or Aluminum Block Set\nMicrocentrifuge Tube, 1.5mL or PCR strips\nSamples\nTwist Enzymatic Fragmentation and Twist Universal Adapter System\nOptional, Single-Well Reservoir, such as the NEST 1-Well Reservoir, 195mL or Agilent 1-Well Reservoir, 290mL, for liquid waste\n\n\n\nDeck Layout\n\nSlot 1: Empty Destination PCR Labware (such as NEST 96-Well PCR Plate or PCR Strips in 96-Well Aluminum Block)\n\nSlot 2: Opentrons Tips for P20\n\nSlot 3: Opentrons Tips for P300\n\nSlot 4: Plate containing Twist UDI Prmer (on Opentrons Temperature Module, if active cooling during protocol)\nSlot 5: Labware containing KAPA HiFi HotStart ReadyMix\n\nSlot 6: Opentrons Tips for P300\n\nSlot 8: Multi-Well Reservoir\nLayout for 12-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 1, samples 1-48 (200\u00b5L per sample)\nA4: Freshly prepared 80% ethanol for wash 1, samples 48-96 (200\u00b5L per sample)\nA5: Freshly prepared 80% ethanol for wash 2, samples 1-48 (200\u00b5L per sample)\nA6: Freshly prepared 80% ethanol for wash 2, samples 48-96 (200\u00b5L per sample)\nA12: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\nLayout for 4-well reservoir:\nA1: DNA Purification Beads (80\u00b5L per sample)\nA2: Freshly prepared 80% ethanol for wash 1, samples 1-96 (200\u00b5L per sample)\nA3: Freshly prepared 80% ethanol for wash 2, samples 1-96 (200\u00b5L per sample)\nA4: Elution solution (water, 10mM Tris-HCl pH, or Buffer EB) (17\u00b5L per sample)\n\nSlot 9: Opentrons Tips for P300\n\nSlot 10: Opentrons Magnetic Module with plate from part two\n\nOptional, Slot 11: Single-Well Reservoir for liquid waste\n\nUsing the customizations field (below), set up your protocol.\n P20 Type: Select the type (Single- or Multi-Channel) to use; P20 should should be mounted on the left mount\n P300 Type: Select the type (Single- or Multi-Channel) to use; P300 should should be mounted on the right mount\n Number of Samples: Specify the number of samples to run (1-96)\n Type of MagDeck: Select which generation (1, 2) magnetic module to use\n Plate on MagDeck: Select which labware type contains samples and is placed on magnetic module\n Module (for cooling): Select whether or not an Opentrons module will be used for active cooling during protocol\n Destination Plate: Select the labware that will be used for the elutions\n Reservor for Reagents: Select which reservoir will be used for reagents\n Kapa Mix Labware: Select the labware that will contain the ligation master mix\n Liquid Waste Destination: Select where liquid waste should be disposed of\n\n", "internal": "21e4d8-pt3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/243973/README.json b/protoBuilds/243973/README.json index 899624b86..fade1cf51 100644 --- a/protoBuilds/243973/README.json +++ b/protoBuilds/243973/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "The deck should be setup as follows:\nOpentrons 20\u00b5L Tips: Slot 11\nOpentrons 300\u00b5L Tips: Slot 10\nNEST 12-Well Reservoir, 15mL: Slot 9\nProtein Plate (Source): Slot 8, containing proteins\nDestination Plate(s): Slots 1-7; plate numbers match slot numbers (Plate 1 in Slot 1, etc.)", - "description": "This protocol automates protein normalization with a CSV input. Additionally, it gives the user the ability to send and receive email notifications at points requiring user intervention.\nUsing the P20 8-Channel Pipette (GEN2) and the P300 8-Channel Pipette (GEN2), diluents are added (based on volume) on up to seven plates with a single set of tips. After the diluents are added, the proteins are transferred with a new tip each time and again based on the volume outlined in the CSV. \nBefore the OT-2 transfers the proteins, the robot will pause and prompt the user to add the plate containing proteins to the deck. If selected, the user will also receive an email when this step occurs. The same process will occur at the end of the protocol, letting the user know that they can remove the samples for downstream applications.\nExplanation of complex parameters below:\n* P300-Multi Mount: Select which mount the P300 8-Channel Pipette (GEN2) is attached to.\n* P20-Multi Mount: Select which mount the P20 8-Channel Pipette (GEN2) is attached to.\n* Number of Destination Plates: Specify the number of destination plates that are used in the protocol. Up to 7 plates can be used.\n* Transfer CSV: Upload the CSV containing the information for normalization. The CSV should have a header row and the following columns (in this order): Source Well, Destination Plate, Destination Well, Sample Volume, Diluent Volume.\n* Email (if notifying): If receiving notifications via email, which email would you like to notify?\n* Email Password: This is the password for the notification email (not your e-mail). The applications engineer that developed the protocol can supply this.\n", + "description": "This protocol automates protein normalization with a CSV input. Additionally, it gives the user the ability to send and receive email notifications at points requiring user intervention.\nUsing the P20 8-Channel Pipette (GEN2) and the P300 8-Channel Pipette (GEN2), diluents are added (based on volume) on up to seven plates with a single set of tips. After the diluents are added, the proteins are transferred with a new tip each time and again based on the volume outlined in the CSV. \nBefore the OT-2 transfers the proteins, the robot will pause and prompt the user to add the plate containing proteins to the deck. If selected, the user will also receive an email when this step occurs. The same process will occur at the end of the protocol, letting the user know that they can remove the samples for downstream applications.\nExplanation of complex parameters below:\n P300-Multi Mount: Select which mount the P300 8-Channel Pipette (GEN2) is attached to.\n P20-Multi Mount: Select which mount the P20 8-Channel Pipette (GEN2) is attached to.\n Number of Destination Plates: Specify the number of destination plates that are used in the protocol. Up to 7 plates can be used.\n Transfer CSV: Upload the CSV containing the information for normalization. The CSV should have a header row and the following columns (in this order): Source Well, Destination Plate, Destination Well, Sample Volume, Diluent Volume.\n Email (if notifying): If receiving notifications via email, which email would you like to notify?\n Email Password: This is the password for the notification email (not your e-mail). The applications engineer that developed the protocol can supply this.\n", "internal": "243973", "labware": "\nOpentrons 20\u00b5L Tips\nOpentrons 300\u00b5L Tips\nNEST 12-Well Reservoir, 15mL\nGreiner Bio-One 96-Well Plate, #650161\n", "markdown": { diff --git a/protoBuilds/245eb2/README.json b/protoBuilds/245eb2/README.json index f16140ee7..2ca6217a7 100644 --- a/protoBuilds/245eb2/README.json +++ b/protoBuilds/245eb2/README.json @@ -5,7 +5,7 @@ "Nucleic Acid Extraction" ] }, - "description": "This protocol automates a nucleic acid extraction using the Opentrons Magnetic Module and incorporates the Axygen 300\u00b5L plate (holding samples and elutes).\n\nThis protocol begins with 20\u00b5L of sample in the Axygen plate and 20\u00b5L of magnetic beads are added and mixed. After removing the supernatant, there are two subsequent washes with ethanol (150\u00b5L per sample). Finally, 50\u00b5L of elution buffer is added to the sample wells and after incubation, the elution is transferred to a second Axygen plate.\n\nBetween 1 and 96 samples can be processed with this protocol using the GEN2 p300 Multi-Channel Pipette. Because the 8-channel pipette is used, the protocol will behave as if a multiple of eight is used (ex. if you select 10 samples, the protocol will behave in the same way as if you selected 16 samples) - please plan reagent consumption accordingly.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nAxygen 300\u00b5L Plate\nReagents (magnetic beads, ethanol, elution buffer)\nSamples\n\n\n\nThe Opentrons Magnetic Module should be placed in slot 6 with an Axygen plate containing samples on top.\n\nThe NEST 12-Well Reservoir should be placed in slot 5 with the following reagnets:\n* Magnetic Beads: Slot 8\n* Ethanol (for wash 1): slot 6 (for samples 1-48), slot 5 (for 48+ samples)\n* Ethanol (for wash 2): slot 4 (for samples 1-48), slot 3 (for 48+ samples)\n* Elution Buffer: slot 1\n\n\nThe NEST 1-Well Reservoir should be placed in slot 9 for liquid waste.\n\nAn empty Axygen plate should be placed in slot 3, for elutes.\n\nThe Opentrons Tiprack(s) will be accessed in the following order: slot 1, slot 2, slot 4, slot 7, slot 10, slot 11. Each tiprack contains 12 columns of tips and this protocol will use 6 columns of tips per column of sample.\n\n\nUsing the customizations field (below), set up your protocol.\n* p300 Multi Mount: Select which mount (left, right) the p300 Multi is attached to.\n* Number of Samples: Specify the number of samples to run (1-96).\n\n", + "description": "This protocol automates a nucleic acid extraction using the Opentrons Magnetic Module and incorporates the Axygen 300\u00b5L plate (holding samples and elutes).\n\nThis protocol begins with 20\u00b5L of sample in the Axygen plate and 20\u00b5L of magnetic beads are added and mixed. After removing the supernatant, there are two subsequent washes with ethanol (150\u00b5L per sample). Finally, 50\u00b5L of elution buffer is added to the sample wells and after incubation, the elution is transferred to a second Axygen plate.\n\nBetween 1 and 96 samples can be processed with this protocol using the GEN2 p300 Multi-Channel Pipette. Because the 8-channel pipette is used, the protocol will behave as if a multiple of eight is used (ex. if you select 10 samples, the protocol will behave in the same way as if you selected 16 samples) - please plan reagent consumption accordingly.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nAxygen 300\u00b5L Plate\nReagents (magnetic beads, ethanol, elution buffer)\nSamples\n\n\n\nThe Opentrons Magnetic Module should be placed in slot 6 with an Axygen plate containing samples on top.\n\nThe NEST 12-Well Reservoir should be placed in slot 5 with the following reagnets:\n Magnetic Beads: Slot 8\n Ethanol (for wash 1): slot 6 (for samples 1-48), slot 5 (for 48+ samples)\n Ethanol (for wash 2): slot 4 (for samples 1-48), slot 3 (for 48+ samples)\n Elution Buffer: slot 1\n\n\nThe NEST 1-Well Reservoir should be placed in slot 9 for liquid waste.\n\nAn empty Axygen plate should be placed in slot 3, for elutes.\n\nThe Opentrons Tiprack(s) will be accessed in the following order: slot 1, slot 2, slot 4, slot 7, slot 10, slot 11. Each tiprack contains 12 columns of tips and this protocol will use 6 columns of tips per column of sample.\n\n\nUsing the customizations field (below), set up your protocol.\n p300 Multi Mount: Select which mount (left, right) the p300 Multi is attached to.\n Number of Samples: Specify the number of samples to run (1-96).\n\n", "internal": "245eb2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/25a03d/README.json b/protoBuilds/25a03d/README.json index ce890562d..bfa690535 100644 --- a/protoBuilds/25a03d/README.json +++ b/protoBuilds/25a03d/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps a 96-well plate with mastermix and DNA with one column for controls. The mastermix is viscous and handled accordingly with air gaps, touch tips, blow outs, delays after aspiration, as well as a decreased pipetting flow rate. Mastermix is added into every third column dependent on how many samples are selected, and the control column is added afterwards. After DNA is added to the mastermix and mixed, 20ul of the solution are transferred to the two subsequent columns following that column of interest.\nExplanation of complex parameters below:\n* Number of Samples (not including controls, 1-24): Specify the number of samples not including controls for this run.\n* Final Plate Labware Type: Specify which piece of labware will be used as the final sample plate for this protocol.\n* Control Plate Labware Type: Specify which piece of labware will be used to hold the control.\n* Aspiration/Dispense Flow rates: Specify the global aspiration/dispense flow rates for the P300 and P20 pipettes. A value of 1.0 is default, a value of 0.5 is 50% of the default flow rate, 1.2 a 20% increase in default flow rate, etc. \n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n* P300 Single-Channel Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n", + "description": "This protocol preps a 96-well plate with mastermix and DNA with one column for controls. The mastermix is viscous and handled accordingly with air gaps, touch tips, blow outs, delays after aspiration, as well as a decreased pipetting flow rate. Mastermix is added into every third column dependent on how many samples are selected, and the control column is added afterwards. After DNA is added to the mastermix and mixed, 20ul of the solution are transferred to the two subsequent columns following that column of interest.\nExplanation of complex parameters below:\n Number of Samples (not including controls, 1-24): Specify the number of samples not including controls for this run.\n Final Plate Labware Type: Specify which piece of labware will be used as the final sample plate for this protocol.\n Control Plate Labware Type: Specify which piece of labware will be used to hold the control.\n Aspiration/Dispense Flow rates: Specify the global aspiration/dispense flow rates for the P300 and P20 pipettes. A value of 1.0 is default, a value of 0.5 is 50% of the default flow rate, 1.2 a 20% increase in default flow rate, etc. \n P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n P300 Single-Channel Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n", "internal": "25a03d", "labware": "\nOpentrons 96 well aluminum block with tube strips\nOpentrons 24 well aluminum block\nCustom tip racks\nCustom 96 well plate\n", "markdown": { diff --git a/protoBuilds/26a414/README.json b/protoBuilds/26a414/README.json index e3a985e41..21c095e51 100644 --- a/protoBuilds/26a414/README.json +++ b/protoBuilds/26a414/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol utilizes a CSV (.csv) file to dictate transfers of two reagents (Guanidine and PBS) to a 384-well plate. Simply upload the properly formatted CSV (examples below), set parameters, then download your protocol for use with the OT-2.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP10 Single Pipette\nP50 Single Pipette\nOpentrons 10\u00b5L Tiprack\nOpentrons 50/300\u00b5L Tiprack\nUSA Scientific 12-Well Reservoir, 22mL\nCorning 384-Well Plate\n\n\n\nFor this protocol, be sure that the pipettes (P10 and P50) are attached.\nUsing the customization fields below, set up your protocol.\n* Transfer CSV: Upload your properly formatted (see below) CSV.\n* P10 Single Mount: Specify which mount the P10 is on (left or right).\n* P50 Single Mount: Specify which mount the P50 is on (left or right).\nNote about CSV\nThe CSV should be formatted like so:\nWell | Guanidine Amount (\u00b5L) | PBS Amount (\u00b5L)\nThe first row (A1, B1, C1) can contain headers (like above) or simply have the desired information. All of the following rows should just have the necessary information.\nLabware Setup\nSlot 1: Opentrons 10\u00b5L Tiprack\nSlot 2: 12-Well Reservoir\n* Column 1: Guanidine Solution\n* Column 2: PBS Solution\nSlot 3: 384-Well Plate\nSlot 4: Opentrons 50/300\u00b5L Tiprack", + "description": "This protocol utilizes a CSV (.csv) file to dictate transfers of two reagents (Guanidine and PBS) to a 384-well plate. Simply upload the properly formatted CSV (examples below), set parameters, then download your protocol for use with the OT-2.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP10 Single Pipette\nP50 Single Pipette\nOpentrons 10\u00b5L Tiprack\nOpentrons 50/300\u00b5L Tiprack\nUSA Scientific 12-Well Reservoir, 22mL\nCorning 384-Well Plate\n\n\n\nFor this protocol, be sure that the pipettes (P10 and P50) are attached.\nUsing the customization fields below, set up your protocol.\n Transfer CSV: Upload your properly formatted (see below) CSV.\n P10 Single Mount: Specify which mount the P10 is on (left or right).\n* P50 Single Mount: Specify which mount the P50 is on (left or right).\nNote about CSV\nThe CSV should be formatted like so:\nWell | Guanidine Amount (\u00b5L) | PBS Amount (\u00b5L)\nThe first row (A1, B1, C1) can contain headers (like above) or simply have the desired information. All of the following rows should just have the necessary information.\nLabware Setup\nSlot 1: Opentrons 10\u00b5L Tiprack\nSlot 2: 12-Well Reservoir\n Column 1: Guanidine Solution\n Column 2: PBS Solution\nSlot 3: 384-Well Plate\nSlot 4: Opentrons 50/300\u00b5L Tiprack", "internal": "26a414", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/26c304/README.json b/protoBuilds/26c304/README.json index 93e092e9e..ce1c7a9e4 100644 --- a/protoBuilds/26c304/README.json +++ b/protoBuilds/26c304/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol preps 3, 384 well control plates for further testing of antibodies as part of a larger ELISA protocol. The protocol can be considered in 3 main parts:\n\nSerial dilution of antibody.\n96 well block prepped with diluent and antibody.\nTransfer of antibody to 3, 384 well control plates.\n\nExplanation of complex parameters below:\n* Mix repetitions: Specify the number of mix repetitions.\n* Mix volume: Specify the mix volume in microliters.\n* Initial volume diluent tubes: Specify the initial volume in both diluent tubes. This is used for liquid height tracking.\n* P1000 aspiration/dispense bottom clearance (mm): Specify the aspiration and dispense clearance from the bottom of the well for the P1000 pipette (to avoid plate pick up). The default value is 1mm from the bottom of the well.\n* Mix height clearance: Specify the height from the bottom of the well to mix (to prevent overflowing).\n* P1000 aspirate/dispense flow rate: Specify the p1000 aspirate and dispense flow rates.\n* Touch tip radius: Describes the proportion of the target well\u2019s radius. When radius=1.0, the pipette tip will move to the edge of the target well; when radius=0.5, it will move to 50% of the well\u2019s radius. Default: 1.0 (100%)\n* Touch tip v-offset: Specify the offset in mm from the top of the well to touch tip A positive offset moves the tip higher above the well, while a negative offset moves it lower into the well Default: -1.0 mm\n* Touch tip speed:Specify the speed for touch tip motion, in mm/s. Default: 60.0 mm/s, Max:80.0 mm/s, Min: 20.0 mm/s\n* P20 Pipette Mount: Specify which mount (left or right) to load your pipette.\n* P1000 Pipette Mount: Specify which mount (left or right) to load your pipette.\n", + "description": "This protocol preps 3, 384 well control plates for further testing of antibodies as part of a larger ELISA protocol. The protocol can be considered in 3 main parts:\n\nSerial dilution of antibody.\n96 well block prepped with diluent and antibody.\nTransfer of antibody to 3, 384 well control plates.\n\nExplanation of complex parameters below:\n Mix repetitions: Specify the number of mix repetitions.\n Mix volume: Specify the mix volume in microliters.\n Initial volume diluent tubes: Specify the initial volume in both diluent tubes. This is used for liquid height tracking.\n P1000 aspiration/dispense bottom clearance (mm): Specify the aspiration and dispense clearance from the bottom of the well for the P1000 pipette (to avoid plate pick up). The default value is 1mm from the bottom of the well.\n Mix height clearance: Specify the height from the bottom of the well to mix (to prevent overflowing).\n P1000 aspirate/dispense flow rate: Specify the p1000 aspirate and dispense flow rates.\n Touch tip radius: Describes the proportion of the target well\u2019s radius. When radius=1.0, the pipette tip will move to the edge of the target well; when radius=0.5, it will move to 50% of the well\u2019s radius. Default: 1.0 (100%)\n Touch tip v-offset: Specify the offset in mm from the top of the well to touch tip A positive offset moves the tip higher above the well, while a negative offset moves it lower into the well Default: -1.0 mm\n Touch tip speed:Specify the speed for touch tip motion, in mm/s. Default: 60.0 mm/s, Max:80.0 mm/s, Min: 20.0 mm/s\n P20 Pipette Mount: Specify which mount (left or right) to load your pipette.\n* P1000 Pipette Mount: Specify which mount (left or right) to load your pipette.\n", "internal": "26c304", "labware": "\nGreiner 384 well plate 200ul\nOpentrons 4-in-1 tube rack - 2x3 grid with Appleton 50mL tubes\nOpentrons 4-in-1 tube rack - 4x6 grid with Axygen 1.7mL tubes\nGreiner 96 well plate 2000ul\nOpentrons 20ul tip rack\nOpentrons 1000ul tip rack\n", "markdown": { diff --git a/protoBuilds/274d2a/README.json b/protoBuilds/274d2a/README.json index 6ba900cd1..05378aeea 100644 --- a/protoBuilds/274d2a/README.json +++ b/protoBuilds/274d2a/README.json @@ -5,7 +5,7 @@ "Cherrypicking" ] }, - "description": "\nCherrypicking, or hit-picking, is a key component of many workflows from high-throughput screening to microbial transfections. With this protocol, you can easily select specific wells in any labware without worrying about missing or selecting the wrong well. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nMicroplates (96-well or 384-well)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nLabware will be loaded automatically by specifying the labware loadname and labware slot in the .csv file. All available empty slots will be filled with the necessary tipracks, and the user will be prompted to refill the tipracks if all are emptied in the middle of the protocol.\nCSV Format\nYour cherrypicking transfers must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). Note that the header line (first row of the .csv file) should also be included!\nHere's an example of how a short cherrypicking protocol should be properly formatted:\nNew Tip,Source Labware,Source Slot,Source Well,Source Aspiration Height Above Bottom (in mm),Dest Labware,Dest Slot,Dest Well,Dest Dispense Height Above Bottom (in mm),Volume (in ul)\nyes,agilent_1_reservoir_290ml,1,A1,1,nest_96_wellplate_100ul_pcr_full_skirt,4,A11,2,1\n,nest_12_reservoir_15ml,2,A1,1,corning_384_wellplate_112ul_flat,5,B11,2,3\nyes,nest_1_reservoir_195ml,3,A1,1,corning_384_wellplate_112ul_flat,5,A12,2,7\nIn the above example, 1\u03bcL will be transferred from 1mm above the bottom of well A1 in an Agilent 1-well 290ml reservoir (slot 1) to well A11 in the destination NEST 96-well plate 100\u00b5l (slot 4) with a new tip. After this, 3\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 12-well 15ml reservoir (slot 2) to well A5 in the destination NEST 96-well plate 100\u00b5l (slot 5) with the same tip. Last, 7\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 1-well 195ml reservoir (slot 3) to well H12 in the destination NEST 96-well plate 100\u00b5l (slot 5) with a new tip.\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV for use with this protocol.\nUsing the customizations fields, below set up your protocol.\n* Transfer .csv File: Upload the .csv file containing your well locations, volumes, and source plate (optional).\n* Pipette Model: Select which pipette you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n* Tip Type: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", + "description": "\nCherrypicking, or hit-picking, is a key component of many workflows from high-throughput screening to microbial transfections. With this protocol, you can easily select specific wells in any labware without worrying about missing or selecting the wrong well. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nMicroplates (96-well or 384-well)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nLabware will be loaded automatically by specifying the labware loadname and labware slot in the .csv file. All available empty slots will be filled with the necessary tipracks, and the user will be prompted to refill the tipracks if all are emptied in the middle of the protocol.\nCSV Format\nYour cherrypicking transfers must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). Note that the header line (first row of the .csv file) should also be included!\nHere's an example of how a short cherrypicking protocol should be properly formatted:\nNew Tip,Source Labware,Source Slot,Source Well,Source Aspiration Height Above Bottom (in mm),Dest Labware,Dest Slot,Dest Well,Dest Dispense Height Above Bottom (in mm),Volume (in ul)\nyes,agilent_1_reservoir_290ml,1,A1,1,nest_96_wellplate_100ul_pcr_full_skirt,4,A11,2,1\n,nest_12_reservoir_15ml,2,A1,1,corning_384_wellplate_112ul_flat,5,B11,2,3\nyes,nest_1_reservoir_195ml,3,A1,1,corning_384_wellplate_112ul_flat,5,A12,2,7\nIn the above example, 1\u03bcL will be transferred from 1mm above the bottom of well A1 in an Agilent 1-well 290ml reservoir (slot 1) to well A11 in the destination NEST 96-well plate 100\u00b5l (slot 4) with a new tip. After this, 3\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 12-well 15ml reservoir (slot 2) to well A5 in the destination NEST 96-well plate 100\u00b5l (slot 5) with the same tip. Last, 7\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 1-well 195ml reservoir (slot 3) to well H12 in the destination NEST 96-well plate 100\u00b5l (slot 5) with a new tip.\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV for use with this protocol.\nUsing the customizations fields, below set up your protocol.\n Transfer .csv File: Upload the .csv file containing your well locations, volumes, and source plate (optional).\n Pipette Model: Select which pipette you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n Tip Type: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", "internal": "274d2a", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/277a3d/README.json b/protoBuilds/277a3d/README.json index a70a0494b..0c57997da 100644 --- a/protoBuilds/277a3d/README.json +++ b/protoBuilds/277a3d/README.json @@ -5,7 +5,7 @@ "Oxford Nanopore 16S Barcoding Kit" ] }, - "deck-setup": "\n* blue: water\n* pink: longamp taq\n* purple: barcodes\n* green: starting samples\n* orange: EtOH\n", + "deck-setup": "\n blue: water\n pink: longamp taq\n purple: barcodes\n green: starting samples\n* orange: EtOH\n", "description": "This protocol performs a semi-automated solution for the Oxford Nanopore 16S Barcoding NGS Prep\n", "internal": "277a3d", "labware": "\nOpentrons 4-in-1 Tube Rack Set with 4x6 insert for 1.5ml Eppendorf tubes\nApplied Biosystems MicroAmp\u2122 Optical 96-Well Reaction Plate #N8010560 seated in MicroAmp\u2122 Splash-Free 96-Well Base #4312063\nOpentrons 20\u00b5L Filter Tips\nOpentrons 200\u00b5L Filter Tips\n", diff --git a/protoBuilds/29414b-ot/README.json b/protoBuilds/29414b-ot/README.json index c33dc6078..d44703374 100644 --- a/protoBuilds/29414b-ot/README.json +++ b/protoBuilds/29414b-ot/README.json @@ -5,7 +5,7 @@ "Calibration" ] }, - "description": "This protocol is designed for testing calibration of the OT-2 with a custom tube holder, holding 500\u00b5L tubes from Simport Scientific, with Opentrons Tips. This protocol can be used for testing the P300 Single Channel Pipette or the P300 Multi Channel Pipette.\nIf testing the P300 Single Channel Pipette, the robot will transfer 5\u00b5L from A1 to A2, A3, and A4 with a 200\u00b5L filter tip. The robot will then make transfers with 200\u00b5L filter tips, first 50\u00b5L from B1 to B2, B3, and B4; then 200\u00b5L from C1, to C2, C3, and C4.\nIf testing the P300 Multi Channel Pipette, the robot will transfer 5\u00b5L from column 1 to column 2, 3, and 4 with 200\u00b5L filter tips. The robot will then make transfers with 200\u00b5L filter tips, first 50\u00b5L from column 5 to column 6, 7, and 8; then 200\u00b5L from column 9 to column 10, 11, and 12.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single Channel Pipette\nP300 Multi Channel Pipette\nOpentrons 200\u00b5L Filter Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\n\n\n\nFor this protocol, be sure that the correct pipette (P300 Single or Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Opentrons 200\u00b5L Filter Tips\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder\nUsing the customization fields below, set up your protocol.\n* Pipette Type: Select either Single Channel or Multi Channel. This will also modify the protocol behavior to the corresponding test protocol.\n* Pipette Mount: Specify which mount the P300 is on (left or right).\n* Touch Tip (After Aspiration): Select yes to perform a touch-tip after aspirating from source well.\n* Touch Tip (After Dispense): Select yes to perform a touch-tip after dispensing into source well.\n", + "description": "This protocol is designed for testing calibration of the OT-2 with a custom tube holder, holding 500\u00b5L tubes from Simport Scientific, with Opentrons Tips. This protocol can be used for testing the P300 Single Channel Pipette or the P300 Multi Channel Pipette.\nIf testing the P300 Single Channel Pipette, the robot will transfer 5\u00b5L from A1 to A2, A3, and A4 with a 200\u00b5L filter tip. The robot will then make transfers with 200\u00b5L filter tips, first 50\u00b5L from B1 to B2, B3, and B4; then 200\u00b5L from C1, to C2, C3, and C4.\nIf testing the P300 Multi Channel Pipette, the robot will transfer 5\u00b5L from column 1 to column 2, 3, and 4 with 200\u00b5L filter tips. The robot will then make transfers with 200\u00b5L filter tips, first 50\u00b5L from column 5 to column 6, 7, and 8; then 200\u00b5L from column 9 to column 10, 11, and 12.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single Channel Pipette\nP300 Multi Channel Pipette\nOpentrons 200\u00b5L Filter Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\n\n\n\nFor this protocol, be sure that the correct pipette (P300 Single or Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Opentrons 200\u00b5L Filter Tips\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder\nUsing the customization fields below, set up your protocol.\n Pipette Type: Select either Single Channel or Multi Channel. This will also modify the protocol behavior to the corresponding test protocol.\n Pipette Mount: Specify which mount the P300 is on (left or right).\n Touch Tip (After Aspiration): Select yes to perform a touch-tip after aspirating from source well.\n Touch Tip (After Dispense): Select yes to perform a touch-tip after dispensing into source well.\n", "internal": "29414b-ot", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/29414b/README.json b/protoBuilds/29414b/README.json index 6ef28434e..2f273e62b 100644 --- a/protoBuilds/29414b/README.json +++ b/protoBuilds/29414b/README.json @@ -5,7 +5,7 @@ "Calibration" ] }, - "description": "This protocol is designed for testing calibration of the OT-2 with a custom tube holder, holding 500\u00b5L tubes from Simport Scientific, and non-standard tips. This protocol can be used for testing the P300 Single Channel Pipette or the P300 Multi Channel Pipette.\nIf testing the P300 Single Channel Pipette, the robot will transfer 5\u00b5L from A1 to A2, A3, and A4 with a 2-20\u00b5L tip. The robot will then make transfers with 20-200\u00b5L tips, first 50\u00b5L from B1 to B2, B3, and B4; then 200\u00b5L from C1, to C2, C3, and C4.\nIf testing the P300 Multi Channel Pipette, the robot will transfer 5\u00b5L from column 1 to column 2, 3, and 4 with 2-20\u00b5L tips. The robot will then make transfers with 20-200\u00b5L tips, first 50\u00b5L from column 5 to column 6, 7, and 8; then 200\u00b5L from column 9 to column 10, 11, and 12.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single Channel Pipette\nP300 Multi Channel Pipette\nFisherbrand 2-20\u00b5L Tips\nFisherbrand 20-200\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\n\n\n\nFor this protocol, be sure that the correct pipette (P300 Single or Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Fisherbrand 2-20\u00b5L Tips\nSlot 2: Fisherbrand 20-200\u00b5L Tips\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder\nUsing the customization fields below, set up your protocol.\n* Pipette Type: Select either Single Channel or Multi Channel. This will also modify the protocol behavior to the corresponding test protocol.\n* Pipette Mount: Specify which mount the P300 is on (left or right).\n", + "description": "This protocol is designed for testing calibration of the OT-2 with a custom tube holder, holding 500\u00b5L tubes from Simport Scientific, and non-standard tips. This protocol can be used for testing the P300 Single Channel Pipette or the P300 Multi Channel Pipette.\nIf testing the P300 Single Channel Pipette, the robot will transfer 5\u00b5L from A1 to A2, A3, and A4 with a 2-20\u00b5L tip. The robot will then make transfers with 20-200\u00b5L tips, first 50\u00b5L from B1 to B2, B3, and B4; then 200\u00b5L from C1, to C2, C3, and C4.\nIf testing the P300 Multi Channel Pipette, the robot will transfer 5\u00b5L from column 1 to column 2, 3, and 4 with 2-20\u00b5L tips. The robot will then make transfers with 20-200\u00b5L tips, first 50\u00b5L from column 5 to column 6, 7, and 8; then 200\u00b5L from column 9 to column 10, 11, and 12.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single Channel Pipette\nP300 Multi Channel Pipette\nFisherbrand 2-20\u00b5L Tips\nFisherbrand 20-200\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\n\n\n\nFor this protocol, be sure that the correct pipette (P300 Single or Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Fisherbrand 2-20\u00b5L Tips\nSlot 2: Fisherbrand 20-200\u00b5L Tips\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder\nUsing the customization fields below, set up your protocol.\n Pipette Type: Select either Single Channel or Multi Channel. This will also modify the protocol behavior to the corresponding test protocol.\n Pipette Mount: Specify which mount the P300 is on (left or right).\n", "internal": "29414b", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/2942dd/README.json b/protoBuilds/2942dd/README.json index e91dc6b71..e6f80e14b 100644 --- a/protoBuilds/2942dd/README.json +++ b/protoBuilds/2942dd/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nOpentrons 200ul filter tips (Deck Slot 10)\nOpentrons 20ul filter tips (Deck Slots 5,11)\n96-tube Fluidx rack with 1 mL Fluidx tubes (Deck Slot 9)\n24-tube Opentrons rack with MTC-3220-SG 2 mL tubes (Deck Slots 7,4,1,8)\n\n\n", - "description": "This protocol uses a p300 single-channel pipette to transfer custom volumes of serum reagent from specified locations in four Opentrons 24-tube racks into specified tubes held in a 96-well rack. A p20 single-channel pipette is then used to tranfer a custom volume of RNase A and 20 percent Tween 20 to the same 96-tube rack locations. Finally, destination tube contents are mixed and the tubes are held at room temperature for 30 minutes. Volumes, rack locations and well locations are specified in a csv file uploaded at the time of protocol download.\nLinks:\n* example input csv\n* Fluidx rack and 1 mL tubes\n* MTC Bio MTC-3220-SG tubes", + "description": "This protocol uses a p300 single-channel pipette to transfer custom volumes of serum reagent from specified locations in four Opentrons 24-tube racks into specified tubes held in a 96-well rack. A p20 single-channel pipette is then used to tranfer a custom volume of RNase A and 20 percent Tween 20 to the same 96-tube rack locations. Finally, destination tube contents are mixed and the tubes are held at room temperature for 30 minutes. Volumes, rack locations and well locations are specified in a csv file uploaded at the time of protocol download.\nLinks:\n example input csv\n Fluidx rack and 1 mL tubes\n* MTC Bio MTC-3220-SG tubes", "internal": "2942dd", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/298069/README.json b/protoBuilds/298069/README.json index dd13f9fda..e281c24ba 100644 --- a/protoBuilds/298069/README.json +++ b/protoBuilds/298069/README.json @@ -5,7 +5,7 @@ "Aliquoting" ] }, - "description": "This protocol performs a custom sample aliquoting workflow by transferring the contents of 2 15ml tubes to 12 2ml tubes each. 300\u00b5l is transferred to each tube, and height tracking is performed automatically so that the pipette does not submerge into the solution in the 15ml tubes.\n\n\n\nOpentrons 4-in-1 tuberack with 3x5 insert for 15ml tubes\nOpentrons 4-in-1 tuberack with 4x6 insert for 2ml tubes\nOpentrons P1000 GEN2 single-channel electronic pipette\nOpentrons 1000\u00b5l tiprack\n\n\n\n3x5 tuberack for 15ml tubes (slot 1):\n* tube A1: solution 1 (filled to at least 10ml mark)\n* tube B1: solution 2 (filled to at least 10ml mark)\n4x6 tuberack for 2ml tubes (slot 2):\n* rows A and B: tubes to receive solution 1\n* rows C and D: tubes to receive solution 2", + "description": "This protocol performs a custom sample aliquoting workflow by transferring the contents of 2 15ml tubes to 12 2ml tubes each. 300\u00b5l is transferred to each tube, and height tracking is performed automatically so that the pipette does not submerge into the solution in the 15ml tubes.\n\n\n\nOpentrons 4-in-1 tuberack with 3x5 insert for 15ml tubes\nOpentrons 4-in-1 tuberack with 4x6 insert for 2ml tubes\nOpentrons P1000 GEN2 single-channel electronic pipette\nOpentrons 1000\u00b5l tiprack\n\n\n\n3x5 tuberack for 15ml tubes (slot 1):\n tube A1: solution 1 (filled to at least 10ml mark)\n tube B1: solution 2 (filled to at least 10ml mark)\n4x6 tuberack for 2ml tubes (slot 2):\n rows A and B: tubes to receive solution 1\n rows C and D: tubes to receive solution 2", "internal": "298069", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/29f643/README.json b/protoBuilds/29f643/README.json index 02813e7ac..2f080ea8c 100644 --- a/protoBuilds/29f643/README.json +++ b/protoBuilds/29f643/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nStandards and Controls will be transferred to the first column of each 96-well plate and their duplicate in the second column. After the Standards and Controls have been added, each sample will be added in duplicate (to the well immediately to the right of the initial target destination). Please see below for an example of the resulting plate layout with one sample.\n", - "description": "This protocol automates the Alpco Insulin ELISA protocol. The protocol begins by transferring aliquots of samples, standards, and controls. The rest of the protocol can be automated or include manual interventions (for wash steps and off-deck incubations). Please note this protocol is currently being optimized.\n\nUpdate: This protocol was updated on September 8, 2022\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples\n* P300 Multi-Channel Mount: Select which mount the P300 Multi-Channel Pipette is attached to (the Single-Channel Pipette should be attached to the opposite mount)", + "description": "This protocol automates the Alpco Insulin ELISA protocol. The protocol begins by transferring aliquots of samples, standards, and controls. The rest of the protocol can be automated or include manual interventions (for wash steps and off-deck incubations). Please note this protocol is currently being optimized.\n\nUpdate: This protocol was updated on September 8, 2022\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples\n P300 Multi-Channel Mount: Select which mount the P300 Multi-Channel Pipette is attached to (the Single-Channel Pipette should be attached to the opposite mount)", "internal": "29f643", "labware": "\nNEST 12-Well Reservoir, 15 mL\nOpentrons Tip Rack, 300 \u00b5L\nOpentrons 24-Well Aluminum Block\nNunc MaxiSorp 96 Well Plate, 250\u00b5L\n", "markdown": { diff --git a/protoBuilds/2a370c/README.json b/protoBuilds/2a370c/README.json index 2834e9d86..8ac8a3ed3 100644 --- a/protoBuilds/2a370c/README.json +++ b/protoBuilds/2a370c/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This is a custom protocol that automates certain steps of the Omega Mag-Bind Bacterial DNA 96 Kit on the OT-2 robot. This kit allows rapid isolation of genomic DNA from bacterial samples.\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P1000 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* Magnetic Module Engage Height: The height the magnets will raise on the magnetic module.\n", + "description": "This is a custom protocol that automates certain steps of the Omega Mag-Bind Bacterial DNA 96 Kit on the OT-2 robot. This kit allows rapid isolation of genomic DNA from bacterial samples.\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P1000 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n Magnetic Module Engage Height: The height the magnets will raise on the magnetic module.\n", "internal": "2a370c", "labware": "\nOpentrons Filter Tips\nPlateOne\u00ae Deep 96-Well 2 mL Polypropylene Plate\n", "markdown": { diff --git a/protoBuilds/2aee74-48-2/README.json b/protoBuilds/2aee74-48-2/README.json index 5e0fb8960..adf6fd1fc 100644 --- a/protoBuilds/2aee74-48-2/README.json +++ b/protoBuilds/2aee74-48-2/README.json @@ -5,8 +5,8 @@ "Olink\u00ae Target 48" ] }, - "deck-setup": "\nNote: all volumes for 48 samples (including controls)\n* green on reservoir (slot 5): 10562.0\u00b5l extension mix\n* blue on incubation plate (slot 2): samples\n", - "description": "Links:\n* Part 1: Incubation\n* Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 2/3: Extension for use with the Olink\u00ae Target 48 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", + "deck-setup": "\nNote: all volumes for 48 samples (including controls)\n green on reservoir (slot 5): 10562.0\u00b5l extension mix\n blue on incubation plate (slot 2): samples\n", + "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 2/3: Extension for use with the Olink\u00ae Target 48 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", "internal": "2aee74", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoir, 15 mL\nOpentrons Filter Tips\n", "markdown": { diff --git a/protoBuilds/2aee74-48-3/README.json b/protoBuilds/2aee74-48-3/README.json index 7ffc96d63..96724fb08 100644 --- a/protoBuilds/2aee74-48-3/README.json +++ b/protoBuilds/2aee74-48-3/README.json @@ -5,8 +5,8 @@ "Olink\u00ae Target 48" ] }, - "deck-setup": "\nNote: all volumes for 48 samples (including controls)\n* purple on primer plate (slot 1): primers\n* blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n", - "description": "Links:\n* Part 1: Incubation\n* Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 3/3: Detection for use with the Olink\u00ae Target 48 protocol for protein biomarker discovery. Primers are transferred to the left 48 wells of the Fluidigm detection plate, and samples are transferred to the right 48 wells. The transfer mapping for these plates is shown in the following image:\n\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", + "deck-setup": "\nNote: all volumes for 48 samples (including controls)\n purple on primer plate (slot 1): primers\n blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n", + "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 3/3: Detection for use with the Olink\u00ae Target 48 protocol for protein biomarker discovery. Primers are transferred to the left 48 wells of the Fluidigm detection plate, and samples are transferred to the right 48 wells. The transfer mapping for these plates is shown in the following image:\n\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", "internal": "2aee74", "labware": "\nFluidigm 96.96 Dynamic Array\u2122 IFC for Gene Expression\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", "markdown": { diff --git a/protoBuilds/2aee74-48/README.json b/protoBuilds/2aee74-48/README.json index d217ffb54..293cf33c0 100644 --- a/protoBuilds/2aee74-48/README.json +++ b/protoBuilds/2aee74-48/README.json @@ -5,8 +5,8 @@ "Olink\u00ae Target 48" ] }, - "deck-setup": "\nNote: all volumes for 48 samples (including controls)\n* blue on sample plate (slot 7): starting samples\n* green on tuberack (slot 8): 400.0\u00b5l incubation mix\n", - "description": "Links:\n* Part 1: Incubation\n* Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 1/3: Incubation for use with the Olink\u00ae Target 48 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", + "deck-setup": "\nNote: all volumes for 48 samples (including controls)\n blue on sample plate (slot 7): starting samples\n green on tuberack (slot 8): 400.0\u00b5l incubation mix\n", + "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 1/3: Incubation for use with the Olink\u00ae Target 48 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", "internal": "2aee74", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", "markdown": { diff --git a/protoBuilds/2aee74-96-2/README.json b/protoBuilds/2aee74-96-2/README.json index 9fd019f82..e53094c79 100644 --- a/protoBuilds/2aee74-96-2/README.json +++ b/protoBuilds/2aee74-96-2/README.json @@ -5,8 +5,8 @@ "Olink\u00ae Target 96" ] }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n* green on reservoir (slot 5): 10562.0\u00b5l extension mix\n* blue on incubation plate (slot 2): samples\n", - "description": "Links:\n* Part 1: Incubation\n* Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 2/3: Extension for use with the Olink\u00ae Target 96 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", + "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n green on reservoir (slot 5): 10562.0\u00b5l extension mix\n blue on incubation plate (slot 2): samples\n", + "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 2/3: Extension for use with the Olink\u00ae Target 96 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", "internal": "2aee74", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoir, 15 mL\nOpentrons Filter Tips\n", "markdown": { diff --git a/protoBuilds/2aee74-96-3/README.json b/protoBuilds/2aee74-96-3/README.json index 5e36bd957..121b95420 100644 --- a/protoBuilds/2aee74-96-3/README.json +++ b/protoBuilds/2aee74-96-3/README.json @@ -5,8 +5,8 @@ "Olink\u00ae Target 96" ] }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n* purple on primer plate (slot 1): samples\n* blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n", - "description": "Links:\n* Part 1: Incubation\n* Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 3/3: Detection for use with the Olink\u00ae Target 96 protocol for protein biomarker discovery. Primers are transferred to the left 96 wells of the Fluidigm detection plate, and samples are transferred to the right 96 wells. The transfer mapping for these plates is shown in the following images:\n\n\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", + "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n purple on primer plate (slot 1): samples\n blue on sample plate (slot 5): samples from extension\n* green on tuberack (slot 9): 790.9\u00b5l detection mix\n", + "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 3/3: Detection for use with the Olink\u00ae Target 96 protocol for protein biomarker discovery. Primers are transferred to the left 96 wells of the Fluidigm detection plate, and samples are transferred to the right 96 wells. The transfer mapping for these plates is shown in the following images:\n\n\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", "internal": "2aee74", "labware": "\nFluidigm 96.96 Dynamic Array\u2122 IFC for Gene Expression\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", "markdown": { diff --git a/protoBuilds/2aee74-96/README.json b/protoBuilds/2aee74-96/README.json index 6c570dab6..0df88e48f 100644 --- a/protoBuilds/2aee74-96/README.json +++ b/protoBuilds/2aee74-96/README.json @@ -5,8 +5,8 @@ "Olink\u00ae Target 96" ] }, - "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n* blue on sample plate (slot 7): starting samples\n* green on tuberack (slot 8): 400.0\u00b5l incubation mix\n", - "description": "Links:\n* Part 1: Incubation\n* Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 1/3: Incubation for use with Olink\u00ae Target 96 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", + "deck-setup": "\nNote: all volumes for 96 samples (including controls)\n blue on sample plate (slot 7): starting samples\n green on tuberack (slot 8): 400.0\u00b5l incubation mix\n", + "description": "Links:\n Part 1: Incubation\n Part 2: Extension\n* Part 3: Detection\nThis protocol accomplishes part 1/3: Incubation for use with Olink\u00ae Target 96 protocol for protein biomarker discovery.\n\nOlink\u00ae is a registered trademark of Olink Proteomics AB. Opentrons is not affiliated with or endorsed by Olink Proteomics AB.\n", "internal": "2aee74", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 Tube Rack Set with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons Filter Tips\n", "markdown": { diff --git a/protoBuilds/2b3642/README.json b/protoBuilds/2b3642/README.json index 0e309567f..dbe8a9523 100644 --- a/protoBuilds/2b3642/README.json +++ b/protoBuilds/2b3642/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: The deck layout shown in the image above will change throughout the protocol as labware is moved around. The image above represents the starting layout of the protocol. Please refer to the protocol steps below for more detailed instructions.", - "description": "This protocol automates various parts of the NEBNext Ultra II DNA Library Preparation Kit for Illumina E7645S using the OT-2 and additional hardware modules. The protocol is divided into five sections which includes the following: End Preparation, Adaptor Ligation, Cleanup of Adaptor-Ligated DNA, PCR Amplication and Cleanup of PCR Reaction.\nThe protocol will also pause at various stages prompting for user intervention to replace reagents, tip racks, and perform centrifugation of reaction mixtures.\nExplanation of complex parameters below:\n* Number of Samples: The total number of samples or reactions being run. This kit supports a maximum of 24 samples. Please enter sample numbers in multiples of 8 (Ex: 8, 16, 24).\n* P300 Multichannel GEN2 Mount Position: The position your P300 Multichannel GEN2 pipette is mounted (Left or Right).\n* P20 Single Channel GEN2 Mount Position: The position your P300 Multichannel GEN2 pipette is mounted (Left or Right).\n* Initial Denaturation Cycles: Number of cycles at 98C for 30 seconds.\n* Denaturation and Annealing/Extension Cycles: Number of cycles at 98C for 10 seconds and 65C for 75 seconds.\n* Final Extension Cycles: Number of cycles at 65C for 5 minutes.\n", + "description": "This protocol automates various parts of the NEBNext Ultra II DNA Library Preparation Kit for Illumina E7645S using the OT-2 and additional hardware modules. The protocol is divided into five sections which includes the following: End Preparation, Adaptor Ligation, Cleanup of Adaptor-Ligated DNA, PCR Amplication and Cleanup of PCR Reaction.\nThe protocol will also pause at various stages prompting for user intervention to replace reagents, tip racks, and perform centrifugation of reaction mixtures.\nExplanation of complex parameters below:\n Number of Samples: The total number of samples or reactions being run. This kit supports a maximum of 24 samples. Please enter sample numbers in multiples of 8 (Ex: 8, 16, 24).\n P300 Multichannel GEN2 Mount Position: The position your P300 Multichannel GEN2 pipette is mounted (Left or Right).\n P20 Single Channel GEN2 Mount Position: The position your P300 Multichannel GEN2 pipette is mounted (Left or Right).\n Initial Denaturation Cycles: Number of cycles at 98C for 30 seconds.\n Denaturation and Annealing/Extension Cycles: Number of cycles at 98C for 10 seconds and 65C for 75 seconds.\n Final Extension Cycles: Number of cycles at 65C for 5 minutes.\n", "internal": "2b3642", "labware": "\nOpentrons Aluminum Block Set\nNEST 12-well 15 mL Reservoir\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 200uL Filter Tips\nOpentrons 20uL Filter Tips\n", "markdown": { diff --git a/protoBuilds/2c83f7/README.json b/protoBuilds/2c83f7/README.json index ed8c4d80a..c0e1070e1 100644 --- a/protoBuilds/2c83f7/README.json +++ b/protoBuilds/2c83f7/README.json @@ -5,7 +5,7 @@ "Zymo Kit" ] }, - "description": "This protocol performs capsule nucleic acid purification according to the Zymo Research Direct-zol-96 RNA MagPrep kit. This protocol has been updated from this protocol (written with APIv1) to APIv2.\n\n\n\nOpentrons magnetic module\nP300 Multi-channel electronic pipette\nOpentrons 300ul tiprack\nBio-Rad Hardshell 96-Well PCR Plate 200ul #HSP9601\nAxygen 96-Deepwell Plate 2.0ml #P-DW-20-C-S\nAgilent 1 Well Reservoir 290mL #201252-100\nUSA Scientific 12-channel Reservoir 22ml #1061-8150\n\n\n\n12-channel reservoir (deck slot 5)\n* channel 1: magbeads vortexed and added to the reservoir immediately before beginning the protocol run\n* channel 2: DNAse\n* channels 3-5: RNA buffer\n* channels 6-8: magbead wash 1\n* channels 9-11: magbead wash 2\n* channel 12: DNAse/RNAse-free water", + "description": "This protocol performs capsule nucleic acid purification according to the Zymo Research Direct-zol-96 RNA MagPrep kit. This protocol has been updated from this protocol (written with APIv1) to APIv2.\n\n\n\nOpentrons magnetic module\nP300 Multi-channel electronic pipette\nOpentrons 300ul tiprack\nBio-Rad Hardshell 96-Well PCR Plate 200ul #HSP9601\nAxygen 96-Deepwell Plate 2.0ml #P-DW-20-C-S\nAgilent 1 Well Reservoir 290mL #201252-100\nUSA Scientific 12-channel Reservoir 22ml #1061-8150\n\n\n\n12-channel reservoir (deck slot 5)\n channel 1: magbeads vortexed and added to the reservoir immediately before beginning the protocol run\n channel 2: DNAse\n channels 3-5: RNA buffer\n channels 6-8: magbead wash 1\n channels 9-11: magbead wash 2\n channel 12: DNAse/RNAse-free water", "internal": "2c83f7", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/2cc59d/README.json b/protoBuilds/2cc59d/README.json index 81bc9a21f..ae0134013 100644 --- a/protoBuilds/2cc59d/README.json +++ b/protoBuilds/2cc59d/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs an ELISA assay between two 96 well plates. For detailed instruction, please see protocol steps below. Stop solution and TMB should only be added when prompted by the protocol upon a pause step. The protocol will automatically pause if it runs out of tips, prompting the user to replace. Tip boxes should always be placed in order of slot 7, 8, and 9 on the deck, even if running low sample numbers. Tip box on slot 9 is always used for 4 wash steps.\nExplanation of complex parameters below:\n* Number of samples (1 to 38): Specify the number of samples for this run. The protocol will run as many columns rounding up on the number of samples provided.\n* P20/P300 Pipette Mounts: Specify which mount (left or right) to host the P20 and P300 pipettes.\n", + "description": "This protocol performs an ELISA assay between two 96 well plates. For detailed instruction, please see protocol steps below. Stop solution and TMB should only be added when prompted by the protocol upon a pause step. The protocol will automatically pause if it runs out of tips, prompting the user to replace. Tip boxes should always be placed in order of slot 7, 8, and 9 on the deck, even if running low sample numbers. Tip box on slot 9 is always used for 4 wash steps.\nExplanation of complex parameters below:\n Number of samples (1 to 38): Specify the number of samples for this run. The protocol will run as many columns rounding up on the number of samples provided.\n P20/P300 Pipette Mounts: Specify which mount (left or right) to host the P20 and P300 pipettes.\n", "internal": "2cc59d", "labware": "\nNEST 12 Well Reservoir\nNEST 1 Well Reservoir\nOpentrons 300ul Tips\nOpentrons 20ul Filter Tips\nOpentrons 4-in-1 tube rack with 1.5mL safe-lock Eppendorf tubes\nGreiner 96 Plate\nCostar 96 Plate\n", "markdown": { diff --git a/protoBuilds/2d7d86/README.json b/protoBuilds/2d7d86/README.json index 4d07b2594..0c2ae5212 100644 --- a/protoBuilds/2d7d86/README.json +++ b/protoBuilds/2d7d86/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocols preps a 384 plate for qPCR processing. 1-14 samples can be selected. If running less than 14 samples, the protocol will pick up the correct number of tips (less than 8) to dispense across all columns in the 384 well plate. Tips are exchanged per source column in the 96 well plate.\nExplanation of complex parameters below:\n* Tip pickup starting column (1-12): Specify which column (1-12) of the tiprack to start picking up tips. If \"3\" is selected, then the tip pickup will start on column 3 of the tip rack. Please ensure the starting tip column and the following tip column are full (16 tips between the selected column and the column after).\n* P20 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P20 Multi-Channel pipette.\n", + "description": "This protocols preps a 384 plate for qPCR processing. 1-14 samples can be selected. If running less than 14 samples, the protocol will pick up the correct number of tips (less than 8) to dispense across all columns in the 384 well plate. Tips are exchanged per source column in the 96 well plate.\nExplanation of complex parameters below:\n Tip pickup starting column (1-12): Specify which column (1-12) of the tiprack to start picking up tips. If \"3\" is selected, then the tip pickup will start on column 3 of the tip rack. Please ensure the starting tip column and the following tip column are full (16 tips between the selected column and the column after).\n P20 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P20 Multi-Channel pipette.\n", "internal": "2d7d86", "labware": "\nOpentrons 20ul Filter tips\nThermofisher 96 well plate\nThermofisher 384 well plate\n", "markdown": { diff --git a/protoBuilds/2d9a0c/README.json b/protoBuilds/2d9a0c/README.json index 5532094b7..b36c5cd2d 100644 --- a/protoBuilds/2d9a0c/README.json +++ b/protoBuilds/2d9a0c/README.json @@ -5,7 +5,7 @@ "Complete PCR Workflow" ] }, - "description": "This protocol transfers buffer and sample to a PCR plate on an Opentrons Thermocycler. Buffer and mastermix is added in between temperature profile steps. Block temperature of the thermocycler is set to the temperature of the last sub-step in each profile incubation step. Lid temperature stays constant throughout the protocol and is specified by the user.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Thermocycler\nP20 Single Pipette\nP300 Single Pipette\nOpentrons 96 Tip Rack 20 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap\nOpentrons 24 Tube Rack with Eppendorf 2 mL Safe-Lock Snapcap\nThermoFisher PCR Plate 96 Well Non Skirted\n\n\n\nFor this protocol, be sure that the pipettes (P20 and P300) are attached.\nUsing the customization fields below, set up your protocol.\n* Lid Temperature: Specify lid temperature to be set for the duration of the protocol (default 105C).\n* Tube rack used: Specify whether you are using 1.5mL or 2mL Eppendorf tube rack.\n* Number of Samples in Plate B: Specify the number of samples to be transferred and ultimately cycled on the 96 well plate on the thermocycler.\n* Number of tip racks: Specify the number of 20\u00b5L tip racks you will have loaded onto the deck.\n* P20 Single Mount: Specify which mount the P10 is on (left or right).\n* P300 Single Mount: Specify which mount the P50 is on (left or right).\nNote about 20\u00b5L tip racks\nYou can upload up to 3 Opentrons 20\u00b5L tip racks for this protocol in slots 1, 2, and 3, respectively. If only loading one tip rack, load it onto Slot 1. If loading two tip racks, load to Slots 1 and 2 and so forth. The protocol will prompt you to replace tips when tips run out - you will need to reload all tip racks to the original configuration at the start of the protocol.\nLabware Setup\nSlots 1, 2, 3: Opentrons 20\u00b5L tip rack(s)\nSlot 4: Thermo Fisher 96 well-plate\nSlot 5: Opentrons 24 Tube Rack with Eppendorf 1.5 or 2mL Safe-Lock Snapcap\nSlot 6: Opentrons 300\u00b5L tip rack\nSlot 7, 8, 10, 11: Opentrons Thermocycler loaded with Thermo Fisher 96 well-plate loaded", + "description": "This protocol transfers buffer and sample to a PCR plate on an Opentrons Thermocycler. Buffer and mastermix is added in between temperature profile steps. Block temperature of the thermocycler is set to the temperature of the last sub-step in each profile incubation step. Lid temperature stays constant throughout the protocol and is specified by the user.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Thermocycler\nP20 Single Pipette\nP300 Single Pipette\nOpentrons 96 Tip Rack 20 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap\nOpentrons 24 Tube Rack with Eppendorf 2 mL Safe-Lock Snapcap\nThermoFisher PCR Plate 96 Well Non Skirted\n\n\n\nFor this protocol, be sure that the pipettes (P20 and P300) are attached.\nUsing the customization fields below, set up your protocol.\n Lid Temperature: Specify lid temperature to be set for the duration of the protocol (default 105C).\n Tube rack used: Specify whether you are using 1.5mL or 2mL Eppendorf tube rack.\n Number of Samples in Plate B: Specify the number of samples to be transferred and ultimately cycled on the 96 well plate on the thermocycler.\n Number of tip racks: Specify the number of 20\u00b5L tip racks you will have loaded onto the deck.\n P20 Single Mount: Specify which mount the P10 is on (left or right).\n P300 Single Mount: Specify which mount the P50 is on (left or right).\nNote about 20\u00b5L tip racks\nYou can upload up to 3 Opentrons 20\u00b5L tip racks for this protocol in slots 1, 2, and 3, respectively. If only loading one tip rack, load it onto Slot 1. If loading two tip racks, load to Slots 1 and 2 and so forth. The protocol will prompt you to replace tips when tips run out - you will need to reload all tip racks to the original configuration at the start of the protocol.\nLabware Setup\nSlots 1, 2, 3: Opentrons 20\u00b5L tip rack(s)\nSlot 4: Thermo Fisher 96 well-plate\nSlot 5: Opentrons 24 Tube Rack with Eppendorf 1.5 or 2mL Safe-Lock Snapcap\nSlot 6: Opentrons 300\u00b5L tip rack\nSlot 7, 8, 10, 11: Opentrons Thermocycler loaded with Thermo Fisher 96 well-plate loaded", "internal": "2d9a0c", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/2df9f8-pt2/README.json b/protoBuilds/2df9f8-pt2/README.json index 76352f6ae..de694815a 100644 --- a/protoBuilds/2df9f8-pt2/README.json +++ b/protoBuilds/2df9f8-pt2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThis is the deck setup for a run with 94 samples (bottom two rows of slot 11 are not populated).\n\n\n", - "description": "This protocol preps a 96 well plate by transferring 6ul from a source plate deepwell plate to a destination deepwell plate.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples (1-94) to run on this protocol. Note: samples will be picked by row in the tube racks, in order of slots 7, 8, 10, and 11.\n* P20 Mount: Specify which side to mount your P20 Multi Channel Pipette.\n", + "description": "This protocol preps a 96 well plate by transferring 6ul from a source plate deepwell plate to a destination deepwell plate.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples (1-94) to run on this protocol. Note: samples will be picked by row in the tube racks, in order of slots 7, 8, 10, and 11.\n P20 Mount: Specify which side to mount your P20 Multi Channel Pipette.\n", "internal": "2df9f8-pt2", "labware": "\nOpentrons 20ul tips\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\n", "markdown": { diff --git a/protoBuilds/2df9f8-pt4/README.json b/protoBuilds/2df9f8-pt4/README.json index 04fab3d6f..7c226cebd 100644 --- a/protoBuilds/2df9f8-pt4/README.json +++ b/protoBuilds/2df9f8-pt4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol pools up to 5 plates by column to a final destination plate. 100ul of sample is taken from each column of each specified plate and dispensed into the final deep well plate on slot 11.\nExplanation of complex parameters below:\n* Number of plates: Specify the number of agar plates (1-5) to fill for this run.\n* Number of columns in each plate: Specify the number of columns (1-12) in each agar plate to fill.\n* P300 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", + "description": "This protocol pools up to 5 plates by column to a final destination plate. 100ul of sample is taken from each column of each specified plate and dispensed into the final deep well plate on slot 11.\nExplanation of complex parameters below:\n Number of plates: Specify the number of agar plates (1-5) to fill for this run.\n Number of columns in each plate: Specify the number of columns (1-12) in each agar plate to fill.\n* P300 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", "internal": "2df9f8-pt4", "labware": "\nNEST 2mL 96 well deep well plate\nOpentrons 300uL Tips\n", "markdown": { diff --git a/protoBuilds/2df9f8/README.json b/protoBuilds/2df9f8/README.json index 9b8e598fa..0ff72293f 100644 --- a/protoBuilds/2df9f8/README.json +++ b/protoBuilds/2df9f8/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThis is the deck setup for a run with 94 samples (bottom two rows of slot 11 are not populated).\n\n\n", - "description": "This protocol preps a 96 well plate with heat inactivated Covid samples and mastermix, for further processing on a Quant-5. A1 and A2 are left for positive and negative conrols. The protocol can be considered in 2 main sections:\n\nMastermix added to 96 well plate\nSamples added to 96 well plate\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples (1-94) to run on this protocol. Note: samples will be picked by row in the tube racks, in order of slots 7, 8, 10, and 11.\n* Plate: Specify whether loading the microamp (I48HO) 96 well plate, or another 96 well plate.\n* P20 Mount: Specify which side to mount your P20 Multi Channel Pipette.\n", + "description": "This protocol preps a 96 well plate with heat inactivated Covid samples and mastermix, for further processing on a Quant-5. A1 and A2 are left for positive and negative conrols. The protocol can be considered in 2 main sections:\n\nMastermix added to 96 well plate\nSamples added to 96 well plate\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples (1-94) to run on this protocol. Note: samples will be picked by row in the tube racks, in order of slots 7, 8, 10, and 11.\n Plate: Specify whether loading the microamp (I48HO) 96 well plate, or another 96 well plate.\n* P20 Mount: Specify which side to mount your P20 Multi Channel Pipette.\n", "internal": "2df9f8", "labware": "\nOpentrons 200ul tips\nMicroamp 200ul well plate\nOpentrons 4-in-1 tuberack with 4x6 tube insert (1.5mL tubes)\n", "markdown": { diff --git a/protoBuilds/2ed4de-2/README.json b/protoBuilds/2ed4de-2/README.json index abade9833..cb49a73d2 100644 --- a/protoBuilds/2ed4de-2/README.json +++ b/protoBuilds/2ed4de-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "This example starting deck state shows the layout for 24 samples:\n\n\ngreen on sample tuberack: samples\nblue on reagent reservoir: working standard\npink on reagent reservoir: assay buffer (TE or TR)\n\n", - "description": "Links:\n* Part 1\n* Part 2\nThis is a protocol for the Flu Ribogreen Assay protocol. Samples are aligned in the sample tuberack (slot 1) in the following order:\n* A1 -> sample 1\n* B1 -> sample 2\n* C1 -> sample 3\n* D1 -> sample 4\n* A2 -> sample 5\n* B2 -> sample 6\n* C2 -> sample 7\n* D2 -> sample 8\n* etc.\n", + "description": "Links:\n Part 1\n Part 2\nThis is a protocol for the Flu Ribogreen Assay protocol. Samples are aligned in the sample tuberack (slot 1) in the following order:\n A1 -> sample 1\n B1 -> sample 2\n C1 -> sample 3\n D1 -> sample 4\n A2 -> sample 5\n B2 -> sample 6\n C2 -> sample 7\n D2 -> sample 8\n* etc.\n", "internal": "2ed4de", "labware": "\nCorning 96 Well Plate 360 \u00b5L Flat\nNEST 12 Well Reservoir 15 mL\nNEST 2 mL 96-Well Deep Well Plate\nOpentrons 24 Tube Rack with Eppendorf 1.5 mL Screwcap Tubes or equivalent\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 1000 \u00b5L\n", "markdown": { diff --git a/protoBuilds/2ed4de/README.json b/protoBuilds/2ed4de/README.json index df8dabf44..b9c9ad410 100644 --- a/protoBuilds/2ed4de/README.json +++ b/protoBuilds/2ed4de/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "This example starting deck state shows the layout for 8 samples:\n\n\ngreen on sample tuberack: samples\nblue on reagent reservoir: working standard 1\npink on reagent reservoir: assay buffer 1 (TE)\npurple on reagent reservoir: working standard 2\norange on reagent reservoir: assay buffer 2 (TR)\n\n", - "description": "Links:\n* Part 1\n* Part 2\nThis is a protocol for the Flu Ribogreen Assay protocol. Samples are aligned in the sample tuberack (slot 1) in the following order:\n* A1 -> sample 1\n* B1 -> sample 2\n* C1 -> sample 3\n* D1 -> sample 4\n* A2 -> sample 5\n* B2 -> sample 6\n* C2 -> sample 7\n* D2 -> sample 8\n", + "description": "Links:\n Part 1\n Part 2\nThis is a protocol for the Flu Ribogreen Assay protocol. Samples are aligned in the sample tuberack (slot 1) in the following order:\n A1 -> sample 1\n B1 -> sample 2\n C1 -> sample 3\n D1 -> sample 4\n A2 -> sample 5\n B2 -> sample 6\n C2 -> sample 7\n D2 -> sample 8\n", "internal": "2ed4de", "labware": "\nCorning 96 Well Plate 360 \u00b5L Flat\nNEST 12 Well Reservoir 15 mL\nNEST 2 mL 96-Well Deep Well Plate\nOpentrons 24 Tube Rack with Eppendorf 1.5 mL Screwcap Tubes or equivalent\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 1000 \u00b5L\n", "markdown": { diff --git a/protoBuilds/2ee5be/README.json b/protoBuilds/2ee5be/README.json index 1973b845b..621666030 100644 --- a/protoBuilds/2ee5be/README.json +++ b/protoBuilds/2ee5be/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol performs PCR prep by reformatting 4 different 96 Well King Fisher plates into a MicroAmp 384 Well PCR plate. It begins by creating an adequate amount of mastermix depending on the number of samples.\n96 Well Plate Format\n\n384 Well Plate Format\n\n\n\n\nP300 single-channel GEN2 electronic pipette\nP20 multi-channel GEN2 electronic pipette\nOpentrons 300ul tiprack\nOpentrons 20ul tiprack\nKingFisher\u2122 Plastics for 96 deep-well format\nMicroAmp\u2122 Optical 384-Well Reaction Plate with Barcode\n\n\n\nDeck Setup\n* KingFisher Deep Well Plates (Slots 1-4)\n* MicroAmp 384 Well PCR Plate (Slot 5)\n* NEST 12 Reservoir 15mL (Slot 6)\n - Water (A1)\n - Multiplex Reagent (A2)\n - Dye (A3)\n* Opentrons 300 uL Tip Rack (Slot 7)\n* Opentrons 200 uL Tip Rack (Slots 8-11)", + "description": "This protocol performs PCR prep by reformatting 4 different 96 Well King Fisher plates into a MicroAmp 384 Well PCR plate. It begins by creating an adequate amount of mastermix depending on the number of samples.\n96 Well Plate Format\n\n384 Well Plate Format\n\n\n\n\nP300 single-channel GEN2 electronic pipette\nP20 multi-channel GEN2 electronic pipette\nOpentrons 300ul tiprack\nOpentrons 20ul tiprack\nKingFisher\u2122 Plastics for 96 deep-well format\nMicroAmp\u2122 Optical 384-Well Reaction Plate with Barcode\n\n\n\nDeck Setup\n KingFisher Deep Well Plates (Slots 1-4)\n MicroAmp 384 Well PCR Plate (Slot 5)\n NEST 12 Reservoir 15mL (Slot 6)\n - Water (A1)\n - Multiplex Reagent (A2)\n - Dye (A3)\n Opentrons 300 uL Tip Rack (Slot 7)\n* Opentrons 200 uL Tip Rack (Slots 8-11)", "internal": "2ee5be", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/300073-2/README.json b/protoBuilds/300073-2/README.json index 89f9a7468..0746ae26d 100644 --- a/protoBuilds/300073-2/README.json +++ b/protoBuilds/300073-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol transfers 5 \u00b5L of saliva samples from a source to a target 96 well plate using a 20 \u00b5L multi-channel pipette.\nThe protocol lets the user control the height of aspiration/dispension from the bottom of the samples and target wells, as well as the flow rate of aspiration and dispension.\nExplanation of parameters below:\n* Number of samples to transfer: How many samples to transfer from the source to the target plate\n* Aspiration flow rate (\u00b5L/s): rate of aspiration in microliters per second\n* Dispension flow rate (\u00b5L/s): rate of dispension in microliters per second\n* Aspiration height from the bottom of the tubes (mm): Height from the bottom of the tubes to aspirate from in mm\n* Dispension height from the bottom of the tubes (mm): Height from the bottom of the plate wells to dispense from in mm\n* (Optional) Temperature module with aluminum block: Parameter to indicate whether you are using a temperature module with an aluminum block to put your source plate on\n* Set temperature of the temperature module: Temperature to set on the temperature module in degrees C\n* Amount of time to keep the pipette in the tube after aspiration (s): How many seconds to wait before withdrawing the pipette from the tube after aspiration\n", + "description": "This protocol transfers 5 \u00b5L of saliva samples from a source to a target 96 well plate using a 20 \u00b5L multi-channel pipette.\nThe protocol lets the user control the height of aspiration/dispension from the bottom of the samples and target wells, as well as the flow rate of aspiration and dispension.\nExplanation of parameters below:\n Number of samples to transfer: How many samples to transfer from the source to the target plate\n Aspiration flow rate (\u00b5L/s): rate of aspiration in microliters per second\n Dispension flow rate (\u00b5L/s): rate of dispension in microliters per second\n Aspiration height from the bottom of the tubes (mm): Height from the bottom of the tubes to aspirate from in mm\n Dispension height from the bottom of the tubes (mm): Height from the bottom of the plate wells to dispense from in mm\n (Optional) Temperature module with aluminum block: Parameter to indicate whether you are using a temperature module with an aluminum block to put your source plate on\n Set temperature of the temperature module: Temperature to set on the temperature module in degrees C\n Amount of time to keep the pipette in the tube after aspiration (s): How many seconds to wait before withdrawing the pipette from the tube after aspiration\n", "internal": "300073-2", "labware": "\nStellar Scientific 96 well plate\n", "markdown": { diff --git a/protoBuilds/300073/README.json b/protoBuilds/300073/README.json index 5fb14927b..52eff89e7 100644 --- a/protoBuilds/300073/README.json +++ b/protoBuilds/300073/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol transfers saliva samples from 25 mL tubes to a 96 well plate. The samples are located in 6 4-in-4 tube racks on the left side of the deck. Optionally a second set of tube racks can replace the first one if more than 45 samples need to be distributed. Optionally the target plate can be placed on a temperature module with an aluminum block.\nThe destination plate is divided into four quadrants and the samples are distributed in a zig zag pattern from top left - top right - bottom left - bottom right (see below). Samples are not transferred to the three first wells of the target plate because they contain control samples, symmetrically the first 3 tube slots in Sample set 1:Tuberack quadrant 1 contain no sample tubes.\nThe tubes in the tuberacks in slot 10, 11, 7 and 8 constitute the 1st tuberack quadrant, and should be regarded as a single unit (Tuberack quadrant 1) consisting of 4 rows of tubes with 12 columns. Samples are transferred in row order to quadrant 1 of the target plate for Sample set 1, and to quadrant 3 for Sample set 2.\nSimilarly the tuberacks in slot 4, 5, 1 and 2 constitute Tuberack quadrant 2. Samples from Sample set 1 in Tuberack quadrant 2 are transferred to Target quadrant 2, and samples from Sample set 2 are transferred to Target quadrant 4.\n96 well-plate layout\n```\nTarget quadrant 1 (top left)\nA1-D1 to A6-D6 (A1-A3 are unused)\nTarget quadrant 2 (top right)\nA7-D7 to A12-D12\nTarget quadrant 3 (bottom left)\nE1-H1 to E6-H6\nTarget quadrant 4 (bottom right)\nE7-H7 to E12-H12\n```\nExplanation of parameters below:\n* Is there a first set of tubes?: Is there a first set of tubes? (Sometimes the user may have already transferred the first set of tubes and wants the protocol to run from the second set of tuberack samples)\n* Number of tubes/samples in the first set of tubes: How many tubes there are in the first set of tube racks. These samples will be transferred to quadrant 1 (and 2) of the destination plate\n* Is there a second set of tubes?: Whether to pause the protocol so that a second set of tube racks can be loaded onto the deck\n* Number of tubes/samples in the second set of tubes: How many samples there are in the second set of tuberacks (Only needs to be set if a second set of tube racks is loaded)\n* Sample volume (\u00b5L) to aspirate: Volume of sample to transfer (5 or 50 \u00b5L). This parameter controls which pipette and tiprack is used: 5 uL means that the 20 uL pipette will be used in in the right mount, and that the pipette tips should be filtered 20 uL tips. 50 uL means that the 300 uL pipette will be used in the left mount along with 200 uL filter tips.\n* Aspiration flow rate (\u00b5L/s): rate of aspiration in microliters per second\n* Dispension flow rate (\u00b5L/s): rate of dispension in microliters per second\n* Aspiration height from the bottom of the tubes (mm): Height from the bottom of the tubes to aspirate from in mm\n* Dispension height from the bottom of the tubes (mm): Height from the bottom of the plate wells to dispense from in mm\n* (Optional) Temperature module with aluminum block: Parameter to indicate whether you are using a temperature module with an aluminum block to put your target plate on\n* Set temperature of the temperature module: Temperature to set on the temperature module in degrees C\n* Amount of time to keep the pipette in the tube after aspiration (s): How many seconds to wait before withdrawing the pipette from the tube after aspiration\n", + "description": "This protocol transfers saliva samples from 25 mL tubes to a 96 well plate. The samples are located in 6 4-in-4 tube racks on the left side of the deck. Optionally a second set of tube racks can replace the first one if more than 45 samples need to be distributed. Optionally the target plate can be placed on a temperature module with an aluminum block.\nThe destination plate is divided into four quadrants and the samples are distributed in a zig zag pattern from top left - top right - bottom left - bottom right (see below). Samples are not transferred to the three first wells of the target plate because they contain control samples, symmetrically the first 3 tube slots in Sample set 1:Tuberack quadrant 1 contain no sample tubes.\nThe tubes in the tuberacks in slot 10, 11, 7 and 8 constitute the 1st tuberack quadrant, and should be regarded as a single unit (Tuberack quadrant 1) consisting of 4 rows of tubes with 12 columns. Samples are transferred in row order to quadrant 1 of the target plate for Sample set 1, and to quadrant 3 for Sample set 2.\nSimilarly the tuberacks in slot 4, 5, 1 and 2 constitute Tuberack quadrant 2. Samples from Sample set 1 in Tuberack quadrant 2 are transferred to Target quadrant 2, and samples from Sample set 2 are transferred to Target quadrant 4.\n96 well-plate layout\n```\nTarget quadrant 1 (top left)\nA1-D1 to A6-D6 (A1-A3 are unused)\nTarget quadrant 2 (top right)\nA7-D7 to A12-D12\nTarget quadrant 3 (bottom left)\nE1-H1 to E6-H6\nTarget quadrant 4 (bottom right)\nE7-H7 to E12-H12\n```\nExplanation of parameters below:\n Is there a first set of tubes?: Is there a first set of tubes? (Sometimes the user may have already transferred the first set of tubes and wants the protocol to run from the second set of tuberack samples)\n Number of tubes/samples in the first set of tubes: How many tubes there are in the first set of tube racks. These samples will be transferred to quadrant 1 (and 2) of the destination plate\n Is there a second set of tubes?: Whether to pause the protocol so that a second set of tube racks can be loaded onto the deck\n Number of tubes/samples in the second set of tubes: How many samples there are in the second set of tuberacks (Only needs to be set if a second set of tube racks is loaded)\n Sample volume (\u00b5L) to aspirate: Volume of sample to transfer (5 or 50 \u00b5L). This parameter controls which pipette and tiprack is used: 5 uL means that the 20 uL pipette will be used in in the right mount, and that the pipette tips should be filtered 20 uL tips. 50 uL means that the 300 uL pipette will be used in the left mount along with 200 uL filter tips.\n Aspiration flow rate (\u00b5L/s): rate of aspiration in microliters per second\n Dispension flow rate (\u00b5L/s): rate of dispension in microliters per second\n Aspiration height from the bottom of the tubes (mm): Height from the bottom of the tubes to aspirate from in mm\n Dispension height from the bottom of the tubes (mm): Height from the bottom of the plate wells to dispense from in mm\n (Optional) Temperature module with aluminum block: Parameter to indicate whether you are using a temperature module with an aluminum block to put your target plate on\n Set temperature of the temperature module: Temperature to set on the temperature module in degrees C\n Amount of time to keep the pipette in the tube after aspiration (s): How many seconds to wait before withdrawing the pipette from the tube after aspiration\n", "internal": "300073", "labware": "\n4-in-1 tube racks\nStellar Scientific 96 well plate\n", "markdown": { diff --git a/protoBuilds/313086-logixsmart-station-B/README.json b/protoBuilds/313086-logixsmart-station-B/README.json index 8ea774403..812063a1a 100644 --- a/protoBuilds/313086-logixsmart-station-B/README.json +++ b/protoBuilds/313086-logixsmart-station-B/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\ngreen: mastermix\npink: positive control\npurple: negative control \nblue: starting samples\n\n\n", - "description": "Links:\n* Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n* Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station B)\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below:\n\n", + "description": "Links:\n Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station B)\nThis protocol performs PCR prep in a NEST 96-well PCR plate. Samples with buffer pre-added should be arranged in a NEST 96-deepwell, and mastermix and controls should be loaded in 1.5ml microcentrifuge tubes in the Opentrons 4x6 tuberack. The transfer order is as shown below:\n\n", "internal": "313086", "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 24 tuberack with NEST 1.5 mL Microcentrifuge Tubes\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 10\u00b5l tipracks\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", "markdown": { diff --git a/protoBuilds/313086/README.json b/protoBuilds/313086/README.json index 3dd174592..a1a9a1bb1 100644 --- a/protoBuilds/313086/README.json +++ b/protoBuilds/313086/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\ngreen: lysis/binding buffer (13ml per channel)\npink: elution buffer: (9ml per channel)\nblue: starting samples\n\n\n", - "description": "Links:\n* Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n* Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station B)\nThis protocol plates lysis/binding buffer, samples, and elution buffer in a NEST 96-deepwell plate. Samples should be arranged in up to 4x Opentrons tuberacks, and buffers should be loaded in a NEST 12-channel reservoir. The transfer order is as shown below:\n\nDeepwells A1 and B1 are left empty for controls to be added later on.\n", + "description": "Links:\n Logix Smart Nasopharyngeal Covid-19 Plating (Station A)\n Logix Smart Nasopharyngeal/Saliva Covid-19 PCR Prep (Station B)\nThis protocol plates lysis/binding buffer, samples, and elution buffer in a NEST 96-deepwell plate. Samples should be arranged in up to 4x Opentrons tuberacks, and buffers should be loaded in a NEST 12-channel reservoir. The transfer order is as shown below:\n\nDeepwells A1 and B1 are left empty for controls to be added later on.\n", "internal": "313086", "labware": "\nNEST 12-Well Reservoirs, 15 mL\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 24 tuberack with NEST 1.5 mL Microcentrifuge Tubes\nOpentrons 300\u00b5l tipracks\nOpentrons 1000\u00b5l tipracks\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com", "markdown": { diff --git a/protoBuilds/32207e/README.json b/protoBuilds/32207e/README.json index bece37470..1f748d1f9 100644 --- a/protoBuilds/32207e/README.json +++ b/protoBuilds/32207e/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps a 96 well plate with up to 96 samples of DNA, normalizing all DNA samples to the same concentration with TE. TE should not be filled more than 20mL in the 50mL falcon tube to prevent pipette plunging. One tip is used to load TE onto the plate, whereas one tip per sample is used for loading DNA samples to plate. After DNA is loaded, DNA and TE are mixed at 80% of the total well volume for 3 repetitions. If a volume greater than 180ul is passed in to the TE volume (greater than well volume), an error is thrown and the protocol will stop. \nExplanation of complex parameters below:\n* .csv file: Please upload your csv file in the following format, header included (no commas in header!). \"Name\" column blocked out for proprietary reasons.\n\n* DNA Aspiration Rate: Specify the rate at which to aspirate DNA. A value of 1 is default, 0.5 being 50% of the default value, 1.2 being 20% faster than the default value, etc.\n* Track tips?: Specify whether to start at A1 of both tip racks, or to start picking up from where the last protocol left off.\n* P20/P300 Mount: Specify which mount (left or right) to host the P20 and P300 single channel pipette.\n", + "description": "This protocol preps a 96 well plate with up to 96 samples of DNA, normalizing all DNA samples to the same concentration with TE. TE should not be filled more than 20mL in the 50mL falcon tube to prevent pipette plunging. One tip is used to load TE onto the plate, whereas one tip per sample is used for loading DNA samples to plate. After DNA is loaded, DNA and TE are mixed at 80% of the total well volume for 3 repetitions. If a volume greater than 180ul is passed in to the TE volume (greater than well volume), an error is thrown and the protocol will stop. \nExplanation of complex parameters below:\n .csv file: Please upload your csv file in the following format, header included (no commas in header!). \"Name\" column blocked out for proprietary reasons.\n\n DNA Aspiration Rate: Specify the rate at which to aspirate DNA. A value of 1 is default, 0.5 being 50% of the default value, 1.2 being 20% faster than the default value, etc.\n Track tips?: Specify whether to start at A1 of both tip racks, or to start picking up from where the last protocol left off.\n P20/P300 Mount: Specify which mount (left or right) to host the P20 and P300 single channel pipette.\n", "internal": "32207e", "labware": "\nOpentrons 4-in-1 Tube Rack with 50mL Falcon Tubes\nOpentrons 300ul Tips\nSarstedt PCR plate full skirt, 96 well, transparent, Low Profile, 100 \u00b5l\n", "markdown": { diff --git a/protoBuilds/3308b4/README.json b/protoBuilds/3308b4/README.json index 872fcd984..156dce4a1 100644 --- a/protoBuilds/3308b4/README.json +++ b/protoBuilds/3308b4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This is a specific protocol for aliquoting liquid from three reagent plates to three 96 deep well plates using a multi-channel p300 pipette. Tips are changed between reagents. Either pipette mount can be specified in setup.\n* 350ul SPR Wash Buffer is added to a 96 deep well plate\n* 350ul VHB Buffer is added to a second 96 deep well plate\n* 50ul nuclease free water is added to a third 96 deep well plate\n\n'P300-Multi Mount Side': Left or right refers to the pipette mount side\n", + "description": "This is a specific protocol for aliquoting liquid from three reagent plates to three 96 deep well plates using a multi-channel p300 pipette. Tips are changed between reagents. Either pipette mount can be specified in setup.\n 350ul SPR Wash Buffer is added to a 96 deep well plate\n 350ul VHB Buffer is added to a second 96 deep well plate\n* 50ul nuclease free water is added to a third 96 deep well plate\n\n'P300-Multi Mount Side': Left or right refers to the pipette mount side\n", "internal": "3308b4", "labware": "\n3x NEST 1 Well Reservoir 195ml\n3x NEST 96 Deepwell Plate 2ml\n", "markdown": { diff --git a/protoBuilds/3359a5/README.json b/protoBuilds/3359a5/README.json index cd0daa616..698d27bf2 100644 --- a/protoBuilds/3359a5/README.json +++ b/protoBuilds/3359a5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Example Deck Setup - this is variable depending on the .csv uploaded.\n\n", - "description": "With this protocol, your robot can perform multiple well-to-well liquid transfers using a single-channel pipette by parsing through a user-defined .csv file. The protocol can use Opentrons GEN1 or GEN2 pipettes.\nThis particular cherrypicking protocol allows you to specify the source plate labware and slot number, as well as the aspiration height above the bottom of the well (in mm). Appropriate tip racks will be placed in every slot that isn't already populated with a source or destination labware.\nExplanation of complex parameters below:\n* Pipette Type: Specify which single channel pipette you will be using for this protocol.\n* input .csv file: Here, you should upload a .csv file formatted in the following way being sure to include the header line. Refer to our Labware Library to copy API names for labware to include in the source_labware and destination_labware columns of the .csv.\n", + "description": "With this protocol, your robot can perform multiple well-to-well liquid transfers using a single-channel pipette by parsing through a user-defined .csv file. The protocol can use Opentrons GEN1 or GEN2 pipettes.\nThis particular cherrypicking protocol allows you to specify the source plate labware and slot number, as well as the aspiration height above the bottom of the well (in mm). Appropriate tip racks will be placed in every slot that isn't already populated with a source or destination labware.\nExplanation of complex parameters below:\n Pipette Type: Specify which single channel pipette you will be using for this protocol.\n input .csv file: Here, you should upload a .csv file formatted in the following way being sure to include the header line. Refer to our Labware Library to copy API names for labware to include in the source_labware and destination_labware columns of the .csv.\n", "internal": "3359a5", "labware": "\nAny verified labware found in our Labware Library\n", "markdown": { diff --git a/protoBuilds/33900b/README.json b/protoBuilds/33900b/README.json index b6846d659..bc78d577d 100644 --- a/protoBuilds/33900b/README.json +++ b/protoBuilds/33900b/README.json @@ -5,7 +5,7 @@ "MagneHis\u2122 Protein Purification System" ] }, - "description": "This protocol performs a custom protein purification on the OT-2 using the Promega MagneHis\u2122 Protein Purification System in conjunction with the Opentrons magnetic module. The user is prompted to replace tipracks once in the protocol if necessary.\n\n\n\nOpentrons magnetic module with Greiner Bio-One 96-deepwell block 2ml #780270\nGreiner Bio-One 96-well PCR plate 200\u00b5l #651161\nAgilent 12-channel reservoir 21ml #201256-100\nAgilent 3-channel reservoir 95ml #204249-100\nOpentrons P300 GEN1 multi-channel electronic pipette\nOpentrons 300ul tipracks\n\n\n\n12-channel reservoir (slot 2, volumes for 96 samples)\n* channel 1: 17ml 10x FastBreak\u2122 Cell Lysis Reagent\n* channel 2: 17ml 10x Benzonase/Lysozyme Mix\n* channel 3: 17ml 5M NaCl\n* channel 4: 10ml MagneHis particles\n* channel 5: 17ml MagneHis Elution Buffer\n* channels 7-10: liquid waste (loaded empty)\n3-channel reservoir (slot 3, volumes for 96 samples)\n* channel 1: 80ml MagneHis Wash Buffer\n* channels 2-3: liquid waste (loaded empty)", + "description": "This protocol performs a custom protein purification on the OT-2 using the Promega MagneHis\u2122 Protein Purification System in conjunction with the Opentrons magnetic module. The user is prompted to replace tipracks once in the protocol if necessary.\n\n\n\nOpentrons magnetic module with Greiner Bio-One 96-deepwell block 2ml #780270\nGreiner Bio-One 96-well PCR plate 200\u00b5l #651161\nAgilent 12-channel reservoir 21ml #201256-100\nAgilent 3-channel reservoir 95ml #204249-100\nOpentrons P300 GEN1 multi-channel electronic pipette\nOpentrons 300ul tipracks\n\n\n\n12-channel reservoir (slot 2, volumes for 96 samples)\n channel 1: 17ml 10x FastBreak\u2122 Cell Lysis Reagent\n channel 2: 17ml 10x Benzonase/Lysozyme Mix\n channel 3: 17ml 5M NaCl\n channel 4: 10ml MagneHis particles\n channel 5: 17ml MagneHis Elution Buffer\n channels 7-10: liquid waste (loaded empty)\n3-channel reservoir (slot 3, volumes for 96 samples)\n channel 1: 80ml MagneHis Wash Buffer\n channels 2-3: liquid waste (loaded empty)", "internal": "33900b", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/33a449/README.json b/protoBuilds/33a449/README.json index 855ab2139..fdb7139e2 100644 --- a/protoBuilds/33a449/README.json +++ b/protoBuilds/33a449/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: reagents in reservoirs are in the order of the colors from left to right.\n\n", - "description": "This protocol extracts DNA using the Nucleomag blood DNA kit. Pro-k is added to sample, as well as bead buffer. Supernatant is removed with magnets engaged before a dispense of 200ul of mbl3. After supernatant is again removed, ethanol is dispensed and removed in wash before mbl5 is added to sample. The final product is moved to the elute plate on slot 2.\nExplanation of complex parameters below:\n* Number of Columns: Specify the number of sample columns to run.\n* Use filter tips: Specify whether this run will use filter tips or regular tips.\n* mbl5 Volume: Specify the mbl5 volume in microliters.\n* Magnetic engage height (mm): Specify the engage height for the magnets to raise under the base of the magnetic plate. The engage height should be empirically tested.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", + "description": "This protocol extracts DNA using the Nucleomag blood DNA kit. Pro-k is added to sample, as well as bead buffer. Supernatant is removed with magnets engaged before a dispense of 200ul of mbl3. After supernatant is again removed, ethanol is dispensed and removed in wash before mbl5 is added to sample. The final product is moved to the elute plate on slot 2.\nExplanation of complex parameters below:\n Number of Columns: Specify the number of sample columns to run.\n Use filter tips: Specify whether this run will use filter tips or regular tips.\n mbl5 Volume: Specify the mbl5 volume in microliters.\n Magnetic engage height (mm): Specify the engage height for the magnets to raise under the base of the magnetic plate. The engage height should be empirically tested.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", "internal": "33a449", "labware": "\nOpentrons 200ul or 300ul tips\nNEST 12 Well Reservoir\nAbgene 96 Well Plate 700ul\nMacherey Nagel 96 Squarewell Block\n", "markdown": { diff --git a/protoBuilds/343001/README.json b/protoBuilds/343001/README.json index e77da08e5..1e8bb1a51 100644 --- a/protoBuilds/343001/README.json +++ b/protoBuilds/343001/README.json @@ -5,7 +5,7 @@ "Zymo Extraction" ] }, - "description": "This protocol performs a Zymo extraction. The protocol splits elutes (up to 48) six columns apart (for ex, wells A1 and A7).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P50 Single-Channel Pipette\nOpentrons P1000 Single-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nOpentrons 1000\u00b5L Tips\nOpentrons Tube Rack, 24-well\nOpentrons Tube Rack, 6-Well\nNEST 1-Channel Reservoir, 195mL\nZymo Elution Plate\nZymo Block Plate\nReagents\nSamples\n\n\n\nSlot 1: Zymo Elution Plate, clean and empty\nSlot 2: Opentrons Tube Rack, 24-well with 2mL Tubes\n* A1: Proteinase K\n* A2: Magbeads\n* B1: DNase/RNase-Free Water\n* B2: DNase/RNase-Free Water\nSlot 3: Opentrons Tube Rack, 6-well with 50mL Falcon Tubes\n* A1: Pathogen DNA/RNA Buffer\n* A2: Wash Buffer 1\n* B2: Wash Buffer 2\n* A3: Ethanol\n* B3: Ethanol\nSlot 4: Opentrons Magnetic Module with 200\u00b5L Sample in Zymo Block Plate\nSlot 5: Opentrons 1000\u00b5L Tips\nSlot 6: Opentrons 1000\u00b5L Tips\nSlot 7: Opentrons 1000\u00b5L Tips\nSlot 8: Opentrons 1000\u00b5L Tips\nSlot 9: Opentrons 50/300\u00b5L Tips\nSlot 10: Opentrons 50/300\u00b5L Tips\nSlot 11: NEST 1-Channel Reservoir, 195mL (for liquid waste)\nUsing the customizations fields, below set up your protocol.\n* Number of Samples: Specify the number of samples (1-48) you'd like to run.\n* P50 Single Mount: Select which mount (left or right) the P50 Single is attached to.\n* P1000 Single Mount: Select which mount (left or right) the P1000 Single is attached to.\n* MagDeck Incubation Time (mins): Specify how long (in minutes) the MagDeck should be engaged to create pellet, before removing supernatant.\n* Water Volume (for elution): Specify how much DNase/RNase-Free Water (in microliters) to add to each sample. This elution volume will then be split in two different wells in equal amounts.", + "description": "This protocol performs a Zymo extraction. The protocol splits elutes (up to 48) six columns apart (for ex, wells A1 and A7).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P50 Single-Channel Pipette\nOpentrons P1000 Single-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nOpentrons 1000\u00b5L Tips\nOpentrons Tube Rack, 24-well\nOpentrons Tube Rack, 6-Well\nNEST 1-Channel Reservoir, 195mL\nZymo Elution Plate\nZymo Block Plate\nReagents\nSamples\n\n\n\nSlot 1: Zymo Elution Plate, clean and empty\nSlot 2: Opentrons Tube Rack, 24-well with 2mL Tubes\n A1: Proteinase K\n A2: Magbeads\n B1: DNase/RNase-Free Water\n B2: DNase/RNase-Free Water\nSlot 3: Opentrons Tube Rack, 6-well with 50mL Falcon Tubes\n A1: Pathogen DNA/RNA Buffer\n A2: Wash Buffer 1\n B2: Wash Buffer 2\n A3: Ethanol\n* B3: Ethanol\nSlot 4: Opentrons Magnetic Module with 200\u00b5L Sample in Zymo Block Plate\nSlot 5: Opentrons 1000\u00b5L Tips\nSlot 6: Opentrons 1000\u00b5L Tips\nSlot 7: Opentrons 1000\u00b5L Tips\nSlot 8: Opentrons 1000\u00b5L Tips\nSlot 9: Opentrons 50/300\u00b5L Tips\nSlot 10: Opentrons 50/300\u00b5L Tips\nSlot 11: NEST 1-Channel Reservoir, 195mL (for liquid waste)\nUsing the customizations fields, below set up your protocol.\n Number of Samples: Specify the number of samples (1-48) you'd like to run.\n P50 Single Mount: Select which mount (left or right) the P50 Single is attached to.\n P1000 Single Mount: Select which mount (left or right) the P1000 Single is attached to.\n MagDeck Incubation Time (mins): Specify how long (in minutes) the MagDeck should be engaged to create pellet, before removing supernatant.\n* Water Volume (for elution): Specify how much DNase/RNase-Free Water (in microliters) to add to each sample. This elution volume will then be split in two different wells in equal amounts.", "internal": "343001", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/357404/README.json b/protoBuilds/357404/README.json index 1c3f3e6b7..34a1d9d73 100644 --- a/protoBuilds/357404/README.json +++ b/protoBuilds/357404/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs immunostaining of slides in a custom 3D printed slide block with Shandon coverplates.\nUp to 7 slide blocks, each with 8 wells can be placed on the deck resulting in the ability to immunostain up to 56 slides simultaneously.\nThe protocol can be stopped after the addition of the block reagent if the user wants to incubate the slides overnight, and can be restarted at the next step which is the addition of the 1st antibody.\nPipette racks and reagents may have to be replaced during the run depending on the number of samples. If that happens the lights on the OT-2 will flash to indicate that the protocol requires the users attention.\nExplanation of parameters below:\n* Number of slide blocks: How many slide holding blocks there are on the deck. The maximum number that will fit on the deck are 7.\n* Number of samples in the last block: All slide blocks except the last one are assumed to be full, however the last block may have a number of samples between 1 and 8\n* Volume in reagents containers: How much volume (\u00b5L) there is in each reagent tube (meaning block, antibody 1, antibody 2, and nuclear counterstain tubes). It is a good idea to have some amount of excess in each tube, about 50-100 uL to account for pipetting variance.\n* Sweep dispense steps: How many discrete step motions + dispenses to do when dispensing reagents and PBS, this is designed to replicate a sweeping motion with a manual pipette while dispensing. For example if the parameter is set to 5 the pipette will cover the length of the Shandon coverplate's mouth in 5 steps and dispense a 5th of the total dispensation volume each time.\n* Reagent tuberack: What type of tuberack you wish to use for the reagents (block, the antibodies and the nuclear counterstain). The maximal number of tubes for any reagents is 4 (a full column, so dimension the tubes accordingly). The maximal required volume for each reagent is 4.9 mL for a full deck (7 blocks8 samples each). This volume would fit for example in 4 1.5 mL tubes.\n* Pipette offset: Pipetting offset in millimeter when dispensing, increasing this parameter will mean that the pipette will dispense at a higher height in the wells, while making it negative will lower the height of dispenses. This parameter must be adjusted carefully so that there are no collisions between the pipette tip and the Shandon coverplates!*\n* Start protocol after 1st incubation step: Starts the protocol at the step after the samples have already been incubated with block overnight.\n* Stop protocol after 1st incubation step: The protocol stops after adding the block reagent and the user is asked to incubate the samples at 4 degrees C overnight.\n* Do a dry run?: Skip all incubation pauses and return tips to their racks after use.\n* Time per block (s): The amount of time it takes to transfer reagent per block. The user must measure the time it takes for the reagent dispensation steps to finish for each block using a stopwatch, for example by putting the maximum of of seven blocks on the deck, running the protocol and then calculating the average block time by dividing by seven. This time is used to subtract from the total incubation time such that each sample will have an hour of incubation instead of 1 hour plus the time it takes to transfer reagent or PBS.\n* Multi-dispense reagents?: Whether to aspirate a 100 uL of reagent at a time and dispense it in the next well or aspirate 900 uL and go from well to well dispensing 100 uL each before picking up more reagent.\n* Reuse reagent tips?: Use the same tip for each individual reagent.\n* Reuse PBS wash tips?: Use one tip to do one wash with PBS\n* Use temperature module?: Whether to use a temperature module to chill the reagents in the tuberack, or put the tuberack directly on the slot.\n* P1000 slot: Which mount to use for the P1000 single GEN2 pipette\n* Reagent tuberack: Which reagent tuberack you want to use in the protocol\n* Well edge offset (mm): The offset from the well's edge when performing the dispensing while moving action. The pipette will start dispensing on one side of the well minus the offset and will travel to the other side of the well minus the same offset.\n* Use a custom slide block: Setting this parameter to Yes means that the protocol will try to load an alternative definition for the slide block. See Custom labware loadName parameter below.\n* Custom labware loadName: Put the labware load name of the alternative slide block labware definition you wish to use. To find the loadName: Open your labware_definition.json file, look for the section \"parameters\"\ne.g.\n\"parameters\": {\n \"format\": \"irregular\",\n \"quirks\": [],\n \"isTiprack\": false,\n \"isMagneticModuleCompatible\": false,\n \"loadName\": \"customslideblockv2_8_wellplate\"\nand copy the value of loadName (without the quotation marks). paste that value into this parameter field, i.e. in this case that would be: customslideblockv2_8_wellplate\nRemember to load the labware into the Opentrons app before running your protocol\n", + "description": "This protocol performs immunostaining of slides in a custom 3D printed slide block with Shandon coverplates.\nUp to 7 slide blocks, each with 8 wells can be placed on the deck resulting in the ability to immunostain up to 56 slides simultaneously.\nThe protocol can be stopped after the addition of the block reagent if the user wants to incubate the slides overnight, and can be restarted at the next step which is the addition of the 1st antibody.\nPipette racks and reagents may have to be replaced during the run depending on the number of samples. If that happens the lights on the OT-2 will flash to indicate that the protocol requires the users attention.\nExplanation of parameters below:\n Number of slide blocks: How many slide holding blocks there are on the deck. The maximum number that will fit on the deck are 7.\n Number of samples in the last block: All slide blocks except the last one are assumed to be full, however the last block may have a number of samples between 1 and 8\n Volume in reagents containers: How much volume (\u00b5L) there is in each reagent tube (meaning block, antibody 1, antibody 2, and nuclear counterstain tubes). It is a good idea to have some amount of excess in each tube, about 50-100 uL to account for pipetting variance.\n Sweep dispense steps: How many discrete step motions + dispenses to do when dispensing reagents and PBS, this is designed to replicate a sweeping motion with a manual pipette while dispensing. For example if the parameter is set to 5 the pipette will cover the length of the Shandon coverplate's mouth in 5 steps and dispense a 5th of the total dispensation volume each time.\n Reagent tuberack: What type of tuberack you wish to use for the reagents (block, the antibodies and the nuclear counterstain). The maximal number of tubes for any reagents is 4 (a full column, so dimension the tubes accordingly). The maximal required volume for each reagent is 4.9 mL for a full deck (7 blocks8 samples each). This volume would fit for example in 4 1.5 mL tubes.\n Pipette offset: Pipetting offset in millimeter when dispensing, increasing this parameter will mean that the pipette will dispense at a higher height in the wells, while making it negative will lower the height of dispenses. This parameter must be adjusted carefully so that there are no collisions between the pipette tip and the Shandon coverplates!\n Start protocol after 1st incubation step: Starts the protocol at the step after the samples have already been incubated with block overnight.\n Stop protocol after 1st incubation step: The protocol stops after adding the block reagent and the user is asked to incubate the samples at 4 degrees C overnight.\n Do a dry run?: Skip all incubation pauses and return tips to their racks after use.\n Time per block (s): The amount of time it takes to transfer reagent per block. The user must measure the time it takes for the reagent dispensation steps to finish for each block using a stopwatch, for example by putting the maximum of of seven blocks on the deck, running the protocol and then calculating the average block time by dividing by seven. This time is used to subtract from the total incubation time such that each sample will have an hour of incubation instead of 1 hour plus the time it takes to transfer reagent or PBS.\n Multi-dispense reagents?: Whether to aspirate a 100 uL of reagent at a time and dispense it in the next well or aspirate 900 uL and go from well to well dispensing 100 uL each before picking up more reagent.\n Reuse reagent tips?: Use the same tip for each individual reagent.\n Reuse PBS wash tips?: Use one tip to do one wash with PBS\n Use temperature module?: Whether to use a temperature module to chill the reagents in the tuberack, or put the tuberack directly on the slot.\n P1000 slot: Which mount to use for the P1000 single GEN2 pipette\n Reagent tuberack: Which reagent tuberack you want to use in the protocol\n Well edge offset (mm): The offset from the well's edge when performing the dispensing while moving action. The pipette will start dispensing on one side of the well minus the offset and will travel to the other side of the well minus the same offset.\n Use a custom slide block: Setting this parameter to Yes means that the protocol will try to load an alternative definition for the slide block. See Custom labware loadName parameter below.\n Custom labware loadName: Put the labware load name of the alternative slide block labware definition you wish to use. To find the loadName: Open your labware_definition.json file, look for the section \"parameters\"\ne.g.\n\"parameters\": {\n \"format\": \"irregular\",\n \"quirks\": [],\n \"isTiprack\": false,\n \"isMagneticModuleCompatible\": false,\n \"loadName\": \"customslideblockv2_8_wellplate\"\nand copy the value of loadName (without the quotation marks). paste that value into this parameter field, i.e. in this case that would be: customslideblockv2_8_wellplate\nRemember to load the labware into the Opentrons app before running your protocol\n", "internal": "357404", "labware": "\nOpentrons tuberacks\nOpentrons tubes & vials\nAgilent 1-Well Reservoir 290 mL\n1000 uL tipracks\nOpentrons aluminum block set (optional)\nAgilent 1-Well Reservoir 290 mL\nCustom 3D printed block for holding Shandon coverplates + slides.\n", "markdown": { diff --git a/protoBuilds/35b1a9/README.json b/protoBuilds/35b1a9/README.json index e5b63b76b..18b708a01 100644 --- a/protoBuilds/35b1a9/README.json +++ b/protoBuilds/35b1a9/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol is designed for transferring BHI to Lysis Buffer with P300 Multi-Channel Pipette. The user has the ability to select the number of samples to run.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Multi Channel Pipette\nFisherbrand 2-20\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\nReagents\n\n\n\nFor this protocol, be sure that the correct pipette (P300-Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Fisherbrand 2-20\u00b5L Tips\nSlot 2: Simport Scientific 500\u00b5L Tubes in Custom Holder (Source)\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder (Destination)\nUsing the customization fields below, set up your protocol.\n* Pipette Mount: Specify which mount the P300-Multi is on (left or right).\n* Number of Samples: Specify how many samples should be transferred (1-96).\n", + "description": "This protocol is designed for transferring BHI to Lysis Buffer with P300 Multi-Channel Pipette. The user has the ability to select the number of samples to run.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Multi Channel Pipette\nFisherbrand 2-20\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\nReagents\n\n\n\nFor this protocol, be sure that the correct pipette (P300-Multi) is attached for the intended test case.\nLabware Setup\nSlot 1: Fisherbrand 2-20\u00b5L Tips\nSlot 2: Simport Scientific 500\u00b5L Tubes in Custom Holder (Source)\nSlot 3: Simport Scientific 500\u00b5L Tubes in Custom Holder (Destination)\nUsing the customization fields below, set up your protocol.\n Pipette Mount: Specify which mount the P300-Multi is on (left or right).\n Number of Samples: Specify how many samples should be transferred (1-96).\n", "internal": "35b1a9", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3607d5-2/README.json b/protoBuilds/3607d5-2/README.json index a70da9492..e59aaf943 100644 --- a/protoBuilds/3607d5-2/README.json +++ b/protoBuilds/3607d5-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nblue: samples \ngreen: binding beads \npink: EtOH \npurple: RSB\n\n\n", - "description": "Links:\n* SPRI 1 & 2\n\n\n* PCR2 Setup\n\n\n* SPRI 3\n\n\n* Normalization and Pooling\n\n\n* Rerack\nThe protocol is broken down into 4 main parts:\n* binding buffer addition to samples\n* bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nThe entire sequence is repeated for a total of 2x.\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\n", + "description": "Links:\n SPRI 1 & 2\n\n\n PCR2 Setup\n\n\n SPRI 3\n\n\n Normalization and Pooling\n\n\n* Rerack\nThe protocol is broken down into 4 main parts:\n binding buffer addition to samples\n bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nThe entire sequence is repeated for a total of 2x.\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\n", "internal": "3607d5", "labware": "\nAbgene Midi 96 Well Plate 800 \u00b5L\nAmplifyt 96 Well Plate 200 \u00b5L\nNEST 12 Well Reservoir 15 mL\nOpentrons 20\u00b5l and 300\u00b5l Tipracks\n", "markdown": { diff --git a/protoBuilds/3607d5-3/README.json b/protoBuilds/3607d5-3/README.json index 9b20bf9c8..c5b813439 100644 --- a/protoBuilds/3607d5-3/README.json +++ b/protoBuilds/3607d5-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nblue: samples \ngreen: binding beads \npink: EtOH \npurple: RSB\n\n\n", - "description": "Links:\n* SPRI 1 & 2\n\n\n* PCR2 Setup\n\n\n* SPRI 3\n\n\n* Normalization and Pooling\n\n\n* Rerack\nThe protocol is broken down into 4 main parts:\n* binding buffer addition to samples\n* bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\n", + "description": "Links:\n SPRI 1 & 2\n\n\n PCR2 Setup\n\n\n SPRI 3\n\n\n Normalization and Pooling\n\n\n* Rerack\nThe protocol is broken down into 4 main parts:\n binding buffer addition to samples\n bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nSamples should be loaded on the magnetic module in an Abgene Midi plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 11) to the elution PCR plate (temperature module, slot 3). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\n", "internal": "3607d5", "labware": "\nAbgene Midi 96 Well Plate 800 \u00b5L\nAmplifyt 96 Well Plate 200 \u00b5L\nNEST 12 Well Reservoir 15 mL\nOpentrons 20\u00b5l and 300\u00b5l Tipracks\n", "markdown": { diff --git a/protoBuilds/3607d5-4/README.json b/protoBuilds/3607d5-4/README.json index 83c42ff9e..1604e2ba6 100644 --- a/protoBuilds/3607d5-4/README.json +++ b/protoBuilds/3607d5-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\ngreen: RSB \nblue: samples \n\n\n", - "description": "Links:\n* SPRI 1 & 2\n\n\n* PCR2 Setup\n\n\n* SPRI 3\n\n\n* Normalization and Pooling\n\n\n* Rerack\nThis is a custom normalization pooling protocol from up to 12 sources to a pooling tube. The input .csv for RSB volume specification should be specified as follows:\nwell,volume rsb\nA1,200\nB1,15\n...\n", + "description": "Links:\n SPRI 1 & 2\n\n\n PCR2 Setup\n\n\n SPRI 3\n\n\n Normalization and Pooling\n\n\n* Rerack\nThis is a custom normalization pooling protocol from up to 12 sources to a pooling tube. The input .csv for RSB volume specification should be specified as follows:\nwell,volume rsb\nA1,200\nB1,15\n...\n", "internal": "3607d5", "labware": "\nOpentrons 20\u00b5l Tiprack\nOpentrons 300\u00b5l Tiprack\nOpentrons 96 Well Aluminum Block\nOpentrons 4-in-1 Tuberack Set\n", "markdown": { diff --git a/protoBuilds/3607d5-5/README.json b/protoBuilds/3607d5-5/README.json index 6cdb03fed..b221c8ff8 100644 --- a/protoBuilds/3607d5-5/README.json +++ b/protoBuilds/3607d5-5/README.json @@ -5,7 +5,7 @@ "Normalization" ] }, - "description": "Links:\n* SPRI 1 & 2\n\n\n* PCR2 Setup\n\n\n* SPRI 3\n\n\n* Normalization and Pooling\n\n\n* Rerack\nThis protocol performs a tip reracking consolidation from 4x 200ul filter tipracks with only rows A and B occupied to one of the racks. A P300 multi-channel pipette is used with offset tip pickups to perform the consolidation.\n", + "description": "Links:\n SPRI 1 & 2\n\n\n PCR2 Setup\n\n\n SPRI 3\n\n\n Normalization and Pooling\n\n\n* Rerack\nThis protocol performs a tip reracking consolidation from 4x 200ul filter tipracks with only rows A and B occupied to one of the racks. A P300 multi-channel pipette is used with offset tip pickups to perform the consolidation.\n", "internal": "3607d5", "labware": "\nOpentrons 200ul Filtertipracks\n", "markdown": { diff --git a/protoBuilds/3607d5/README.json b/protoBuilds/3607d5/README.json index 7bc3b2145..042429165 100644 --- a/protoBuilds/3607d5/README.json +++ b/protoBuilds/3607d5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\ngreen: PCR2 buffer \nblue: samples \npink: UDI\n\n\n", - "description": "Links:\n* SPRI 1 & 2\n\n\n* PCR2 Setup\n\n\n* SPRI 3\n\n\n* Normalization and Pooling\n\n\n* Rerack\nIn this protocol, indexes are transferred to their corresponding wells in a PCR plate containing samples. Then, PCR2 buffer is added to each sample and mixed using fresh tips for each transfer.\n", + "description": "Links:\n SPRI 1 & 2\n\n\n PCR2 Setup\n\n\n SPRI 3\n\n\n Normalization and Pooling\n\n\n* Rerack\nIn this protocol, indexes are transferred to their corresponding wells in a PCR plate containing samples. Then, PCR2 buffer is added to each sample and mixed using fresh tips for each transfer.\n", "internal": "3607d5", "labware": "\nAbgene Midi 96 Well Plate 800 \u00b5L\nAmplifyt 96 Well Plate 200 \u00b5L\nOpentrons 20\u00b5l and 300\u00b5l Tipracks\n", "markdown": { diff --git a/protoBuilds/3633ca/README.json b/protoBuilds/3633ca/README.json index 6dc2a17a9..3641c880e 100644 --- a/protoBuilds/3633ca/README.json +++ b/protoBuilds/3633ca/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol adds and removes ethanol to a plate on the Magnetic Module.\n\nThe protocol adds 150\u00b5L of ethanol to each well, using the P300 Multi-Channel pipette, waits 30 seconds, then removes the ethanol and discards the tips. After doing this a second time, the P20 Multi-Channel pipette aspirates 15\u00b5L of liquid from the wells and disposes of it.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module\nOpentrons P300 Multi-Channel Pipette\n(2) Opentrons 300\u00b5L Tips\nOpentrons P20 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nNEST 96-Well Plates\nUSA Scientific 12-Well Reservoir\n\n\n\nSlot 1: USA Scientific 12-Well Reservoir with ethanol in slots 1-4\nSlot 3: Opentrons 20\u00b5L Tips\nSlot 4: Opentrons Magnetic Module with NEST 96-Well Plates\nSlot 7: Opentrons 300\u00b5L Tips\nSlot 10: Opentrons 300\u00b5L Tips\n\n\nUsing the customizations field (below), set up your protocol.\n* P300-Multi Pipette Mount: Select which mount (left or right) the P300-Multi is attached to.\n* P20-Multi Pipette Mount: Select which mount (left or right) the P20-Multi is attached to.", + "description": "This protocol adds and removes ethanol to a plate on the Magnetic Module.\n\nThe protocol adds 150\u00b5L of ethanol to each well, using the P300 Multi-Channel pipette, waits 30 seconds, then removes the ethanol and discards the tips. After doing this a second time, the P20 Multi-Channel pipette aspirates 15\u00b5L of liquid from the wells and disposes of it.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module\nOpentrons P300 Multi-Channel Pipette\n(2) Opentrons 300\u00b5L Tips\nOpentrons P20 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nNEST 96-Well Plates\nUSA Scientific 12-Well Reservoir\n\n\n\nSlot 1: USA Scientific 12-Well Reservoir with ethanol in slots 1-4\nSlot 3: Opentrons 20\u00b5L Tips\nSlot 4: Opentrons Magnetic Module with NEST 96-Well Plates\nSlot 7: Opentrons 300\u00b5L Tips\nSlot 10: Opentrons 300\u00b5L Tips\n\n\nUsing the customizations field (below), set up your protocol.\n P300-Multi Pipette Mount: Select which mount (left or right) the P300-Multi is attached to.\n P20-Multi Pipette Mount: Select which mount (left or right) the P20-Multi is attached to.", "internal": "3633ca", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/37190e/README.json b/protoBuilds/37190e/README.json index fc3ce88b5..bdd3dcba9 100644 --- a/protoBuilds/37190e/README.json +++ b/protoBuilds/37190e/README.json @@ -5,7 +5,7 @@ "Cell Culture" ] }, - "deck-setup": " \nTuberack on slot 9:\n* tube A1: drug A\n* tube A2: drug B\n* tube A3: media\n", + "deck-setup": " \nTuberack on slot 9:\n tube A1: drug A\n tube A2: drug B\n* tube A3: media\n", "description": "This protocol performs a custom cell culture assay on up to 8 flat well plates. Please see these instructions for the exact transfer scheme.\n", "internal": "37190e", "labware": "\nCorning 96 Well Plate 360 \u00b5L Flat, 3650\nOpentrons 10 Tube Rack with NEST 4x50 mL, 6x15 mL Conical\nOpentrons 200\u00b5L Filter Tips\nOpentrons 20\u00b5L Filter Tips\n", diff --git a/protoBuilds/37de37/README.json b/protoBuilds/37de37/README.json index 478c666ae..09b627ce3 100644 --- a/protoBuilds/37de37/README.json +++ b/protoBuilds/37de37/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol normalizes DNA transfers with diluent via a user imported .csv. Diluent is transferred to all relevent wells, and then DNA is premixed (from up to 3 source plates) and added to the diluent well, post-mixed, and pooled in H12 of the final plate.\nExplanation of complex parameters below:\n* .CSV File: : Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\nSample number,Plate number, Source well, Destination well, Start Concentration (ug/uL) Source, Final Concentration (ug/ml) Destination, Sample volume (uL), Diluent Volume(ul), Total Volume(ul) Destination\nNOTE: Plate number in the .csv file (column 2) should be either 1, 2, or 3, since the protocol can handle up to 3 source plates.\n* Number of Source Plates: Specify the number of source plate in this protocol.\n* P20 Single-Channel Mount: Specify which mount (left or right) to mount the Opentrons P20 Single Channel pipette.\n", + "description": "This protocol normalizes DNA transfers with diluent via a user imported .csv. Diluent is transferred to all relevent wells, and then DNA is premixed (from up to 3 source plates) and added to the diluent well, post-mixed, and pooled in H12 of the final plate.\nExplanation of complex parameters below:\n .CSV File: : Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\nSample number,Plate number, Source well, Destination well, Start Concentration (ug/uL) Source, Final Concentration (ug/ml) Destination, Sample volume (uL), Diluent Volume(ul), Total Volume(ul) Destination\nNOTE: Plate number in the .csv file (column 2) should be either 1, 2, or 3, since the protocol can handle up to 3 source plates.\n Number of Source Plates: Specify the number of source plate in this protocol.\n* P20 Single-Channel Mount: Specify which mount (left or right) to mount the Opentrons P20 Single Channel pipette.\n", "internal": "37de37", "labware": "\nCorning 384 Well Plate 360 \u00b5L\nBrooks Life Sciences 21mL 15-well reservoir\nOpentrons 20uL Tips\n", "markdown": { diff --git a/protoBuilds/384b23-plate-transfer/README.json b/protoBuilds/384b23-plate-transfer/README.json index 8ea06ca15..54c1eaa1f 100644 --- a/protoBuilds/384b23-plate-transfer/README.json +++ b/protoBuilds/384b23-plate-transfer/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol transfers 200\u00b5L from vials in 24 tube tuberacks to a 96-well plate. New tips are granted between each transfer. Transfers are completed by column in each tube rack starting at the tube rack in slot 1.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P1000 Single-Channel Pipette\nOpentrons 1000\u00b5L Filter Tip Rack\nOpentrons 200\u00b5L Filter Tips\nCustom Opentrons 24-tube tube rack\n\n\n\nSlots 1, 4, 7, 10: Custom 24-tube tube rack\nSlot 2: 96-well plate\nSlot 3: Opentrons 200\u00b5L Filter Tip Rack\nSlot 5: Opentrons 1000\u00b5L Filter Tip Rack\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify number of samples in the source plate to be transferred. Note, samples should be put in tube racks by column starting from the tube rack in Slot 1. The tube rack in Slot 1 will be transferred down by column before the tube rack in Slot 4 is transferred, and so on.\n* Volume Dispensed: Specify the volume (in microliters) to transfer from the tube rack to the plate. A value greater than 100 will use the P1000 pipette. A value less than 100 will use the P300 pipette. \n* Delay Time after Aspirating (in seconds): Since saliva is being transferred, often times a delay after aspiration allows the pipette to achieve the full volume. Specify the amount of time in seconds after each aspiration (a value of 0 can be inputted).\n* Aspiration Height: Specify the height (in mm) from the bottom of the tubes the pipette will aspirate from.\n P1000 Single GEN2 Mount*: Specify the mount side for the P300 Single GEN2 pipette", + "description": "This protocol transfers 200\u00b5L from vials in 24 tube tuberacks to a 96-well plate. New tips are granted between each transfer. Transfers are completed by column in each tube rack starting at the tube rack in slot 1.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P1000 Single-Channel Pipette\nOpentrons 1000\u00b5L Filter Tip Rack\nOpentrons 200\u00b5L Filter Tips\nCustom Opentrons 24-tube tube rack\n\n\n\nSlots 1, 4, 7, 10: Custom 24-tube tube rack\nSlot 2: 96-well plate\nSlot 3: Opentrons 200\u00b5L Filter Tip Rack\nSlot 5: Opentrons 1000\u00b5L Filter Tip Rack\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify number of samples in the source plate to be transferred. Note, samples should be put in tube racks by column starting from the tube rack in Slot 1. The tube rack in Slot 1 will be transferred down by column before the tube rack in Slot 4 is transferred, and so on.\n Volume Dispensed: Specify the volume (in microliters) to transfer from the tube rack to the plate. A value greater than 100 will use the P1000 pipette. A value less than 100 will use the P300 pipette. \n Delay Time after Aspirating (in seconds): Since saliva is being transferred, often times a delay after aspiration allows the pipette to achieve the full volume. Specify the amount of time in seconds after each aspiration (a value of 0 can be inputted).\n Aspiration Height: Specify the height (in mm) from the bottom of the tubes the pipette will aspirate from.\n* P1000 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette", "internal": "384b23-96-plate-transfer", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/384b23-pooling/README.json b/protoBuilds/384b23-pooling/README.json index cd7b1b70f..bfb9da32a 100644 --- a/protoBuilds/384b23-pooling/README.json +++ b/protoBuilds/384b23-pooling/README.json @@ -5,7 +5,7 @@ "Normalization and Pooling" ] }, - "description": "This protocol pools 100\u00b5L from wells across each row to the recipient tube in column 6 of the respective row (total of 500\u00b5L in each recipient tube).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Single-Channel Pipette\nOpentrons 200\u00b5L Filter Tip Rack\nOpentrons 200\u00b5L Filter Tips\nCustom Opentrons 6x5 tube racks\n\n\n\nSlots 1 (if applicable): Tuberack A\nSlot 2 (if applicable): Tuberack B\nSlot 4: Opentrons 200\u00b5L Filter Tip Rack\n\n\nUsing the customizations field (below), set up your protocol.\n* Using Tuberack A (tubes T1, T2, T3): Specify if Tuberack A will be pooled.\n* Tuberack A tubes: Specify whether you will be populating Tuberack A with T1-T3 tubes or T7 tubes. Leave as is if not using Tuberack A.\n* Number of pooling rows for Tuberack A: Specify how many rows to pool (1-5).\n* Using Tuberack B (tubes T4, T5, T6): Specify if Tuberack B will be pooled\n* Tuberack B tubes: Specify whether you will be populating tuberack B with T4 & T5 tubes or T6 tubes. Leave as is if not using Tuberack B.\n* Number of pooling rows for Tuberack B: Specify how many rows to pool (1-5).\n* Delay Time after Aspirating (in seconds): Since saliva is being transferred, often times a delay after aspiration allows the pipette to achieve the full volume. Specify the amount of time in seconds after each aspiration (a value of 0 can be inputted).\n* P300 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette\n* P300 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette", + "description": "This protocol pools 100\u00b5L from wells across each row to the recipient tube in column 6 of the respective row (total of 500\u00b5L in each recipient tube).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Single-Channel Pipette\nOpentrons 200\u00b5L Filter Tip Rack\nOpentrons 200\u00b5L Filter Tips\nCustom Opentrons 6x5 tube racks\n\n\n\nSlots 1 (if applicable): Tuberack A\nSlot 2 (if applicable): Tuberack B\nSlot 4: Opentrons 200\u00b5L Filter Tip Rack\n\n\nUsing the customizations field (below), set up your protocol.\n Using Tuberack A (tubes T1, T2, T3): Specify if Tuberack A will be pooled.\n Tuberack A tubes: Specify whether you will be populating Tuberack A with T1-T3 tubes or T7 tubes. Leave as is if not using Tuberack A.\n Number of pooling rows for Tuberack A: Specify how many rows to pool (1-5).\n Using Tuberack B (tubes T4, T5, T6): Specify if Tuberack B will be pooled\n Tuberack B tubes: Specify whether you will be populating tuberack B with T4 & T5 tubes or T6 tubes. Leave as is if not using Tuberack B.\n Number of pooling rows for Tuberack B: Specify how many rows to pool (1-5).\n Delay Time after Aspirating (in seconds): Since saliva is being transferred, often times a delay after aspiration allows the pipette to achieve the full volume. Specify the amount of time in seconds after each aspiration (a value of 0 can be inputted).\n P300 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette\n* P300 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette", "internal": "384b23-pooling", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/384b23-tube-transfer/README.json b/protoBuilds/384b23-tube-transfer/README.json index d82e94784..ca2ceba2f 100644 --- a/protoBuilds/384b23-tube-transfer/README.json +++ b/protoBuilds/384b23-tube-transfer/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol transfers 500\u00b5L from tubes in 24 tube tuberacks to a 6x5 tube rack. New tips are granted between each transfer. Transfers are completed by column in the source tube rack and dispensed by row to the recipient tube racks. A new row starts with each column.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P1000 Single-Channel Pipette\nOpentrons 1000\u00b5L Filter Tip Rack\nCustom Opentrons 24-tube tube rack\nCustom Opentrons 30-tube tube rack\n\n\n\nSlots 1: Source tube rack (6x4)\nSlot 2: Destination tube rack (6x5)\nSlot 3: Opentrons 1000\u00b5L Filter Tip Rack\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify number of samples in the source tube rack to be transferred.\n* Delay Time after Aspirating (in seconds): Since saliva is being transferred, often times a delay after aspiration allows the pipette to achieve the full volume. Specify the amount of time in seconds after each aspiration (a value of 0 can be inputted).\n* Aspiration Height for Recipient tube: Specify the height (in mm) from the bottom of the tubes in the recipient tube rack the pipette will aspirate from. Change this value if switching between T4, T5, or T6 tubes.\n* Dispense Height for Recipient tube: Specify the height (in mm) from the bottom of the tubes in the destination tube rack the pipette will dispense at.\n P1000 Single GEN2 Mount*: Specify the mount side for the P300 Single GEN2 pipette", + "description": "This protocol transfers 500\u00b5L from tubes in 24 tube tuberacks to a 6x5 tube rack. New tips are granted between each transfer. Transfers are completed by column in the source tube rack and dispensed by row to the recipient tube racks. A new row starts with each column.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P1000 Single-Channel Pipette\nOpentrons 1000\u00b5L Filter Tip Rack\nCustom Opentrons 24-tube tube rack\nCustom Opentrons 30-tube tube rack\n\n\n\nSlots 1: Source tube rack (6x4)\nSlot 2: Destination tube rack (6x5)\nSlot 3: Opentrons 1000\u00b5L Filter Tip Rack\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify number of samples in the source tube rack to be transferred.\n Delay Time after Aspirating (in seconds): Since saliva is being transferred, often times a delay after aspiration allows the pipette to achieve the full volume. Specify the amount of time in seconds after each aspiration (a value of 0 can be inputted).\n Aspiration Height for Recipient tube: Specify the height (in mm) from the bottom of the tubes in the recipient tube rack the pipette will aspirate from. Change this value if switching between T4, T5, or T6 tubes.\n Dispense Height for Recipient tube: Specify the height (in mm) from the bottom of the tubes in the destination tube rack the pipette will dispense at.\n* P1000 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette", "internal": "384b23-tube-transfer", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/387961/README.json b/protoBuilds/387961/README.json index 71b661a52..5a196e787 100644 --- a/protoBuilds/387961/README.json +++ b/protoBuilds/387961/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol automates the filling of a specialized 384-well (rotated 90 degrees and takes up two slots). Using a 96-well plate containing the reagents, the p20 will aspirate 20\u00b5L from the 96-well plate and dispense 10\u00b5L into the 384-well plate, swapping tips each time the the p20 moves to another column (different reagents) until the 384-well plate is filled.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 Multi-Channel Pipette (attached to right mount)\nOpentrons 20\u00b5L Tip Rack\nNEST 96-Well PCR Plate\n384-Well Plate with Custom Adapter\n\n\n\nDeck Layout\n\nSlot 1: Opentrons 20\u00b5L Tip Rack\n\nSlot 5: NEST 96-Well PCR Plate\nReagent Locations\n* Reagent 1: B1 (40\u00b5L), H11 (160\u00b5L), and H12 (160\u00b5L)\n* Reagent 2: B2 (40\u00b5L), G11 (160\u00b5L), and G12 (160\u00b5L)\n* Reagent 3: A1 (40\u00b5L), F11 (160\u00b5L), and F12 (160\u00b5L)\n* Reagent 4: B3 (40\u00b5L), E11 (160\u00b5L), and E12 (160\u00b5L)\n* Reagent 5: B4 (40\u00b5L), D11 (160\u00b5L), and D12 (160\u00b5L)\n* Reagent 6: A3 (40\u00b5L), C11 (160\u00b5L), and C12 (160\u00b5L)\n* Reagent 7: B6 (40\u00b5L), B11 (160\u00b5L), and B12 (160\u00b5L)\n* Reagent 8: B5 (40\u00b5L), A11 (160\u00b5L), and A12 (160\u00b5L)\n* Reagent 9: D1-D8 + B8 (40\u00b5L)\n* Reagent 10: C1-C8 + B7 (40\u00b5L)\n\nSlot 3/6: 384-Well Plate with Custom Adapter", + "description": "This protocol automates the filling of a specialized 384-well (rotated 90 degrees and takes up two slots). Using a 96-well plate containing the reagents, the p20 will aspirate 20\u00b5L from the 96-well plate and dispense 10\u00b5L into the 384-well plate, swapping tips each time the the p20 moves to another column (different reagents) until the 384-well plate is filled.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p20 Multi-Channel Pipette (attached to right mount)\nOpentrons 20\u00b5L Tip Rack\nNEST 96-Well PCR Plate\n384-Well Plate with Custom Adapter\n\n\n\nDeck Layout\n\nSlot 1: Opentrons 20\u00b5L Tip Rack\n\nSlot 5: NEST 96-Well PCR Plate\nReagent Locations\n Reagent 1: B1 (40\u00b5L), H11 (160\u00b5L), and H12 (160\u00b5L)\n Reagent 2: B2 (40\u00b5L), G11 (160\u00b5L), and G12 (160\u00b5L)\n Reagent 3: A1 (40\u00b5L), F11 (160\u00b5L), and F12 (160\u00b5L)\n Reagent 4: B3 (40\u00b5L), E11 (160\u00b5L), and E12 (160\u00b5L)\n Reagent 5: B4 (40\u00b5L), D11 (160\u00b5L), and D12 (160\u00b5L)\n Reagent 6: A3 (40\u00b5L), C11 (160\u00b5L), and C12 (160\u00b5L)\n Reagent 7: B6 (40\u00b5L), B11 (160\u00b5L), and B12 (160\u00b5L)\n Reagent 8: B5 (40\u00b5L), A11 (160\u00b5L), and A12 (160\u00b5L)\n Reagent 9: D1-D8 + B8 (40\u00b5L)\n Reagent 10: C1-C8 + B7 (40\u00b5L)\n\nSlot 3/6: 384-Well Plate with Custom Adapter", "internal": "387961", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/38efd4/README.json b/protoBuilds/38efd4/README.json index b2b978588..d047415a2 100644 --- a/protoBuilds/38efd4/README.json +++ b/protoBuilds/38efd4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nOpentrons p300 and p1000 tips (Deck Slots 10, 11)\nCrystallization Plate usascientific_96_wellplate_2.4ml_deep (Deck Slot 9)\nDeck Slots 1-8 will either be empty or contain any of the following labware (based on selections made from the pulldown list at the time of protocol download) opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical, opentrons_15_tuberack_falcon_15ml_conical, opentrons_24_tuberack_eppendorf_1.5ml_safelock_snapcap, opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap, opentrons_6_tuberack_falcon_50ml_conical.\n\n\n", - "description": "This protocol uses p300 single channel and p1000 single channel pipettes to transfer and mix custom volumes (ranging from 20 ul - 2 mL specified in input csv file) of water and each of up to 8 stock reagents to the wells of a 96-deep-well plate followed by optional mixing of the well contents.\nLinks:\n* example reagent csv\n* example formulation csv\n* supplemental information spreadsheet\nThis protocol was developed to combine and mix custom volumes (specified in input csv file) of water and up to 8 stock reagents for the screening of protein crystallization conditions in support of protein structure studies.", + "description": "This protocol uses p300 single channel and p1000 single channel pipettes to transfer and mix custom volumes (ranging from 20 ul - 2 mL specified in input csv file) of water and each of up to 8 stock reagents to the wells of a 96-deep-well plate followed by optional mixing of the well contents.\nLinks:\n example reagent csv\n example formulation csv\n* supplemental information spreadsheet\nThis protocol was developed to combine and mix custom volumes (specified in input csv file) of water and up to 8 stock reagents for the screening of protein crystallization conditions in support of protein structure studies.", "internal": "38efd4", "markdown": { "author": "[Opentrons](https://opentrons.com/), Ricardo Padua, Brandeis University\n\n", diff --git a/protoBuilds/3955db/README.json b/protoBuilds/3955db/README.json index c5b68e9e2..564096fc4 100644 --- a/protoBuilds/3955db/README.json +++ b/protoBuilds/3955db/README.json @@ -5,7 +5,7 @@ "Pooling" ] }, - "description": "This flexible protocol automates the pooling of samples in 12mL tubes and the transfer of pooled samples to Visby device for rapid Covid testing.\n\n\n\nProtocol Steps\n1. The protocol begins by pooling samples (1-5) from Tube Racks in slots 2 and 3 into tubes in slot 5.\n2. Once all samples are pooled appropriately, total volume of pooled samples will be added from pooled sample to Visby.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nP1000 Single-Channel GEN2\nOpentrons 1000\u00b5L Filter Tips\nVisby Device with Adapter\nCustom Tube Rack with 12mL Tubes\n\n\n\n\nDeck Layout\n\n\n\n\nExplanation of adjustable parameters below:\n* P1000 Single GEN2 Mount: Select which mount (left, right) the pipette is attached to.\n* Total Volume of Pooled Samples: Specify the volume (in \u00b5L) that should be transferred to the Visby. This volume will be divided by the Number of Samples per Pool to determine how much volume from each individual sample when creating the pools. Example: if this is set to 500 and there are 5 samples per pool, 100\u00b5L will be transferred from each individual sample to the pooled sample tube, then 500\u00b5L of the pooled volume will be added to the Visby.\n* Number of Visbys: Select the number of Visbys (1-6).\n* Number of Samples per Pool: Select the number of samples to pool into one tube (2-5).", + "description": "This flexible protocol automates the pooling of samples in 12mL tubes and the transfer of pooled samples to Visby device for rapid Covid testing.\n\n\n\nProtocol Steps\n1. The protocol begins by pooling samples (1-5) from Tube Racks in slots 2 and 3 into tubes in slot 5.\n2. Once all samples are pooled appropriately, total volume of pooled samples will be added from pooled sample to Visby.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nP1000 Single-Channel GEN2\nOpentrons 1000\u00b5L Filter Tips\nVisby Device with Adapter\nCustom Tube Rack with 12mL Tubes\n\n\n\n\nDeck Layout\n\n\n\n\nExplanation of adjustable parameters below:\n P1000 Single GEN2 Mount: Select which mount (left, right) the pipette is attached to.\n Total Volume of Pooled Samples: Specify the volume (in \u00b5L) that should be transferred to the Visby. This volume will be divided by the Number of Samples per Pool to determine how much volume from each individual sample when creating the pools. Example: if this is set to 500 and there are 5 samples per pool, 100\u00b5L will be transferred from each individual sample to the pooled sample tube, then 500\u00b5L of the pooled volume will be added to the Visby.\n Number of Visbys: Select the number of Visbys (1-6).\n Number of Samples per Pool: Select the number of samples to pool into one tube (2-5).", "internal": "3955db", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3b0db0/README.json b/protoBuilds/3b0db0/README.json index c01bf2646..0d21bca97 100644 --- a/protoBuilds/3b0db0/README.json +++ b/protoBuilds/3b0db0/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol distributes reliance One Step Mulitplex RT-qPCR supermix to each well on a cool (4C) 96 well plate. After, saliva samples from custom Opentrons tube racks are distributed to each well containing mastermix, with a mix step to follow.\nExplanation of complex parameters below:\n* Number of columns: Specify the number of samples (wholly divisible by 8) that the OT-2 will distribute mastermix to on the 96 well plate (1-96).\n* Delay after aspiration: Specify the number of seconds after aspirating for the pipette to pause to achieve full volumes.\n* Mix repetitions: Specify the number of times to mix the mastermix and saliva.\n* Tube Aspiration Height: Specify the aspiration height from the bottom of the tube (in mm) to aspirate from when transferring saliva in the final step.\n* Tube-Strip Aspiration Height for Multi Channel: Specify the aspiration height from the bottom of the tube strip that the multi-channel pipette visits.\n* Aspiration/Dispense Rate: Specify the aspiration/dispense rate for the single and multi-channel pipettes. A value of 1 returns the default speed, 0.5 would return half of the default speed, etc. \n* P20 Multi GEN2 Mount: Specify the mount (left or right) of the P20 Multi GEN2 Pipette.\n* P20 Single GEN2 Mount: Specify the mount (left or right) of the P20 single GEN2 Pipette.\n", + "description": "This protocol distributes reliance One Step Mulitplex RT-qPCR supermix to each well on a cool (4C) 96 well plate. After, saliva samples from custom Opentrons tube racks are distributed to each well containing mastermix, with a mix step to follow.\nExplanation of complex parameters below:\n Number of columns: Specify the number of samples (wholly divisible by 8) that the OT-2 will distribute mastermix to on the 96 well plate (1-96).\n Delay after aspiration: Specify the number of seconds after aspirating for the pipette to pause to achieve full volumes.\n Mix repetitions: Specify the number of times to mix the mastermix and saliva.\n Tube Aspiration Height: Specify the aspiration height from the bottom of the tube (in mm) to aspirate from when transferring saliva in the final step.\n Tube-Strip Aspiration Height for Multi Channel: Specify the aspiration height from the bottom of the tube strip that the multi-channel pipette visits.\n Aspiration/Dispense Rate: Specify the aspiration/dispense rate for the single and multi-channel pipettes. A value of 1 returns the default speed, 0.5 would return half of the default speed, etc. \n P20 Multi GEN2 Mount: Specify the mount (left or right) of the P20 Multi GEN2 Pipette.\n P20 Single GEN2 Mount: Specify the mount (left or right) of the P20 single GEN2 Pipette.\n", "internal": "3b0db0", "labware": "\nBiorad 96 well plate 200ul\nPCR tube strips\nOpentrons custom 4x6 3D printed tube racks\n", "markdown": { diff --git a/protoBuilds/3b3d2f/README.json b/protoBuilds/3b3d2f/README.json index 50778f956..f2dcb29d3 100644 --- a/protoBuilds/3b3d2f/README.json +++ b/protoBuilds/3b3d2f/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nOpentrons p20 filter tips (Deck Slots 10, 11)\nOpentrons Temperature Module (with opentrons_24_aluminumblock_nest_2ml_snapcap Deck Slot 3)\nddPCR Plate (biorad_96_wellplate_200ul_pcr Deck Slot 5)\n", - "description": "This protocol uses a p20 single channel pipette to load (in triplicate) up to four 96-well plates (loading of each plate will be finished before loading of the next plate is started) in preparation for ddPCR from 2 mL source tubes containing reagent mix, water, up to 27 template samples and a positive control template sample (CSV-formatted plate maps are uploaded at the time of protocol download to specify the location and number of sample and control tubes).\nLinks:\n* SOP_SARS-CoV2 in sewage Rose Lab_MSU_v2021draft_06.18.21\n* Sample Plate Map CSV File\n* Sample Plate Map CSV File\nThis protocol was developed to perform the ddPCR plate loading part of the attached SOP for up to four ddPCR plates according to uploaded plate maps formatted as seen in the attached examples (based on plate map examples from Appendix A of the attached SOP).", + "description": "This protocol uses a p20 single channel pipette to load (in triplicate) up to four 96-well plates (loading of each plate will be finished before loading of the next plate is started) in preparation for ddPCR from 2 mL source tubes containing reagent mix, water, up to 27 template samples and a positive control template sample (CSV-formatted plate maps are uploaded at the time of protocol download to specify the location and number of sample and control tubes).\nLinks:\n SOP_SARS-CoV2 in sewage Rose Lab_MSU_v2021draft_06.18.21\n Sample Plate Map CSV File\n* Sample Plate Map CSV File\nThis protocol was developed to perform the ddPCR plate loading part of the attached SOP for up to four ddPCR plates according to uploaded plate maps formatted as seen in the attached examples (based on plate map examples from Appendix A of the attached SOP).", "internal": "3b3d2f", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3c9aec/README.json b/protoBuilds/3c9aec/README.json index 284314242..28441204b 100644 --- a/protoBuilds/3c9aec/README.json +++ b/protoBuilds/3c9aec/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps a 96 well plate with cell culture and a variety of reagents. First, the protocol parses the csv to check for wells which have a confluency value of greater than 85. These values will be referenced and added to for the duration of the protocol. If there are a group of confluency wells with a value of greater than 85 in a single column, the multi-channel pipette will be used, only picking up the number of tips necessary. The user may be asked to replace tips if the protocol runs out. Note that a volume of at least 3mL of any reagent should be in each reservoir well AFTER the protocol is completed (i.e. there should never be > 3mL of reagent at any point of the protocol). See protocol steps below for details.\nExplanation of complex parameters below:\n* csv file: Upload the csv file as so:\nWell,Confluency\nA1, 90\nB1, 83\n* Temperature module temperature (C): Specify temperature module temperatre in celsius\n* First step aspiration rate (moving to waste): Specify the aspiration rate in step 1 of the protocol when included wells are moved to waste, where 1.0 is default, 1.5 is 50% faster, and 0.2 is 20% default speed, for example.\n* PBS Dispense Flow Rate: The PBS will be dispesed into the plate 2mm from the side of the well to avoid separation of culture. Specify the flow rate, where 1.0 is default, 1.5 is 50% faster, and 0.2 is 20% default speed, for example.\n* Incubation Time (minutes): Specify the incubation time i nminutes after trypsin is added to the plate.\n* Media Aspirate X (ul): Specify volume of media to move from column 12 of the reservoir to the plate.\n* Media Dispense Y (ul): Specify the volume of the second media to be added to the plate.\n* Track tips?: Yes for tracking tips, no for fresh tip boxes.\n* P300 Single-Channel Mount: Specify which mount (left or right) to host your P300 pipettes.\n", + "description": "This protocol preps a 96 well plate with cell culture and a variety of reagents. First, the protocol parses the csv to check for wells which have a confluency value of greater than 85. These values will be referenced and added to for the duration of the protocol. If there are a group of confluency wells with a value of greater than 85 in a single column, the multi-channel pipette will be used, only picking up the number of tips necessary. The user may be asked to replace tips if the protocol runs out. Note that a volume of at least 3mL of any reagent should be in each reservoir well AFTER the protocol is completed (i.e. there should never be > 3mL of reagent at any point of the protocol). See protocol steps below for details.\nExplanation of complex parameters below:\n csv file: Upload the csv file as so:\nWell,Confluency\nA1, 90\nB1, 83\n Temperature module temperature (C): Specify temperature module temperatre in celsius\n First step aspiration rate (moving to waste): Specify the aspiration rate in step 1 of the protocol when included wells are moved to waste, where 1.0 is default, 1.5 is 50% faster, and 0.2 is 20% default speed, for example.\n PBS Dispense Flow Rate: The PBS will be dispesed into the plate 2mm from the side of the well to avoid separation of culture. Specify the flow rate, where 1.0 is default, 1.5 is 50% faster, and 0.2 is 20% default speed, for example.\n Incubation Time (minutes): Specify the incubation time i nminutes after trypsin is added to the plate.\n Media Aspirate X (ul): Specify volume of media to move from column 12 of the reservoir to the plate.\n Media Dispense Y (ul): Specify the volume of the second media to be added to the plate.\n Track tips?: Yes for tracking tips, no for fresh tip boxes.\n* P300 Single-Channel Mount: Specify which mount (left or right) to host your P300 pipettes.\n", "internal": "3c9ec", "labware": "\nCorning 360ul 96 well plate flat\nNEST 12 well Reseroir 195mL\nOpentrons 200ul Filter Tips\n", "markdown": { diff --git a/protoBuilds/3cf31f/README.json b/protoBuilds/3cf31f/README.json index 462ae3416..0b49eee89 100644 --- a/protoBuilds/3cf31f/README.json +++ b/protoBuilds/3cf31f/README.json @@ -5,7 +5,7 @@ "Distribution" ] }, - "description": "This protocol is part 1 of 2-part protocol designed to transfer biofluids and add the necessary reagents for preparation. In this part, The biofluids are distributed from cryovials to centrifuge tubes and two solutions are added. The samples are then transferred to a Nanosep 3k Ultrafiltration tube in preparation of centrifugation. See below for deck and reagent setup.\n\n\n\nP300 Single-channel electronic pipette\nP50 Single-channel electronic pipette\n50/300uL Opentrons tipracks\nOpentrons Temperature Module\nOpentrons aluminum block set\nCryovials (containing samples)\n0.5mL centrifuge tubes (clean and empty)\nNanosep 3K Ultrafiltration tubes (clean and empty)\nCustom container for holding cryovials\nCustom container for holding centrifuge tubes (x2)\n\n\n\nSlot 1/4/7: Custom container for holding centrifuge tubes, filled with Nanosep 3k Ultrafiltration tubes\nSlot 2/5/8: Custom container for holding centrifuge tubes, filled with 0.5mL centrifuge tubes\nSlot 3/6/9: Custom container for holding cryovials, filled with cryovials containing samples\nSlot 10: Temperature Module with 24-Well Aluminum Block :\n* A1: Solution 1\n* A2: Solution 2\n* A3: Solution 2\n* A4: Solution 2\n* B1: Solution 2\n* B2: Solution 2\nSlot 11: 50/300ul Opentrons tiprack", + "description": "This protocol is part 1 of 2-part protocol designed to transfer biofluids and add the necessary reagents for preparation. In this part, The biofluids are distributed from cryovials to centrifuge tubes and two solutions are added. The samples are then transferred to a Nanosep 3k Ultrafiltration tube in preparation of centrifugation. See below for deck and reagent setup.\n\n\n\nP300 Single-channel electronic pipette\nP50 Single-channel electronic pipette\n50/300uL Opentrons tipracks\nOpentrons Temperature Module\nOpentrons aluminum block set\nCryovials (containing samples)\n0.5mL centrifuge tubes (clean and empty)\nNanosep 3K Ultrafiltration tubes (clean and empty)\nCustom container for holding cryovials\nCustom container for holding centrifuge tubes (x2)\n\n\n\nSlot 1/4/7: Custom container for holding centrifuge tubes, filled with Nanosep 3k Ultrafiltration tubes\nSlot 2/5/8: Custom container for holding centrifuge tubes, filled with 0.5mL centrifuge tubes\nSlot 3/6/9: Custom container for holding cryovials, filled with cryovials containing samples\nSlot 10: Temperature Module with 24-Well Aluminum Block :\n A1: Solution 1\n A2: Solution 2\n A3: Solution 2\n A4: Solution 2\n B1: Solution 2\n B2: Solution 2\nSlot 11: 50/300ul Opentrons tiprack", "internal": "3cf31f", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3d942d/README.json b/protoBuilds/3d942d/README.json index adacce9fe..671e338ac 100644 --- a/protoBuilds/3d942d/README.json +++ b/protoBuilds/3d942d/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSlot 1: Source Plate (NEST 96-Well Plate)\n\n\nSlot 2: Preamp Plate (NEST 96-Well Plate)\n\n\nSlot 3: Loading Plate (Corning 384-Well Plate)\n\n\nSlot 4: Opentrons 20\u00b5L Filter Tips (Tiprack 1)\n\n\nSlot 5: Opentrons Tube Rack with 24-Tube Topper\n\n\nSlot 7: Opentrons 20\u00b5L Filter Tips (Tiprack 2)\n\n\nSlot 10: Opentrons 20\u00b5L Filter Tips (Tiprack 3)\n\n", - "description": "Theis protocol is used to set up DNA samples for analysis with Life Technologies QuantStudio\u2122 12K Flex Real-Time PCR System, OpenArray\u2122 block, Accufill\u2122 System. Using the P20 Single-Channel Pipette (GEN2), two PCR preps are accomplished. During the first prep, samples are reformatted and transferred from a 96-well plate to another 96-well plate before amplification. Once amplification is complete, the user returns the amplified plate and the second prep occurs - this time samples are transferred from the 96-well plate to a 384-well plate.\nExplanation of complex parameters below:\n* Transfer CSV: CSV file that contains the transfer information. It should contain the following header: SourcePos,SampleID,PreampPos,LoadPos1,LoadPos2\n* P20 Single Mount: Select which mount the P20 Single-Channel Pipette (GEN2) is attached to.\nNote: In the current configuration, up to 95 samples can be completed in one run.\n", + "description": "Theis protocol is used to set up DNA samples for analysis with Life Technologies QuantStudio\u2122 12K Flex Real-Time PCR System, OpenArray\u2122 block, Accufill\u2122 System. Using the P20 Single-Channel Pipette (GEN2), two PCR preps are accomplished. During the first prep, samples are reformatted and transferred from a 96-well plate to another 96-well plate before amplification. Once amplification is complete, the user returns the amplified plate and the second prep occurs - this time samples are transferred from the 96-well plate to a 384-well plate.\nExplanation of complex parameters below:\n Transfer CSV: CSV file that contains the transfer information. It should contain the following header: SourcePos,SampleID,PreampPos,LoadPos1,LoadPos2\n P20 Single Mount: Select which mount the P20 Single-Channel Pipette (GEN2) is attached to.\nNote: In the current configuration, up to 95 samples can be completed in one run.\n", "internal": "3d942d", "labware": "\nOpentrons 20\u00b5L Filter Tips\nNEST 96-Well Plate\nCorning 384-Well Plate\nOpentrons Tube Rack\n1.5mL Microcentrigue Tubes\n", "markdown": { @@ -28,7 +28,7 @@ "pipettes": "\nP20 Single-Channel Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions), if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\nThe user will be prompted to load the Source Plate and Preamp Plate (if not already loaded) and make sure that enough Preamp Mastermix is in the tube in A1 of the Tube Rack.\nThe P20 will pick up a tip, then distribute 2.5\u00b5L of Preamp Mastermix to all wells listed in the PreampPos column of the Transfer CSV. The P20 will mix the Mastermix two times, aspirate 20\u00b5L, then dispense 2.5\u00b5L in each well, repeating this process until complete. When done, the pipette will return any extra Mastermix to the tube, then drop the tip.\nFor each location in SourcePos and PreampPos, the P20 will pick up a tip, go to the SourcePos and mix three times, transfer 2.5\u00b5L to the PreampPos, mix three times, then drop the tip.\nOnce all transfers are completed for the above step, the user will be prompted to remove the plate for amplification. When ready to begin part two, the user will be prompted to load the Preamp Plate and Loading Plate (if not already loaded) and make sure that enough OpenArray Mastermix is in the tube in D6 of the Tube Rack.\nThe P20 will pick up a tip, then distribute 3.75\u00b5L of OpenArray Mastermix to all wells listed in the LoadPos1 and LoadPos2 columns of the Transfer CSV. The P20 will mix the Mastermix two times, aspirate 15\u00b5L, then dispense 3.75\u00b5L in each well, repeating this process until complete. When done, the pipette will return any extra Mastermix to the tube, then drop the tip.\nFor each line of the Transfer CSV, the P20 will pick up a tip, go to the PreampPos and mix three times, transfer 1.75\u00b5L to the LoadPos1, mix three times, then drop the tip. This process will be repeated with the LoadPos2\nOnce complete, the user will be alerted that they can move on to the next step of the process (off deck).\n", - "reagent-setup": "Opentrons Tube Rack with 24-Tube Topper + 1.5mL Microcentrigue Tubes\n* Well A1: Preamp Mastermix\n* Well D6: OpenArray Mastermix\n", + "reagent-setup": "Opentrons Tube Rack with 24-Tube Topper + 1.5mL Microcentrigue Tubes\n Well A1: Preamp Mastermix\n Well D6: OpenArray Mastermix\n", "reagents": [ "Preamp Mastermix", "OpenArray Mastermix" diff --git a/protoBuilds/3db190-manual/README.json b/protoBuilds/3db190-manual/README.json index e7c868909..5ac1f60cd 100644 --- a/protoBuilds/3db190-manual/README.json +++ b/protoBuilds/3db190-manual/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol automates certain steps of the Lyra Direct SARS-CoV Assay. This protocol assumes buffer is being added manually. The automated steps include mixing of the deep well block, and transferring samples to the PCR plate. \n\n\n\nP20 single-channel GEN2 electronic pipette\nP1000 single-channel GEN2 electronic pipette\nOpentrons 20ul filter tiprack\nOpentrons 1000ul filter tiprack\nMicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plates\nEppendorf 96 Deep Well Block 1000ul\n\n\n\nDeck Setup\n* Opentrons 1000ul filter tiprack (Slot 4)\n* Opentrons 20ul filter tiprack (Slot 7)\n* Eppendorf 96 Deep Well Block 1000ul (Slot 2)\n* MicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plate (Slot 3, should be rested on top of the Eppendorf cooling block)", + "description": "This protocol automates certain steps of the Lyra Direct SARS-CoV Assay. This protocol assumes buffer is being added manually. The automated steps include mixing of the deep well block, and transferring samples to the PCR plate. \n\n\n\nP20 single-channel GEN2 electronic pipette\nP1000 single-channel GEN2 electronic pipette\nOpentrons 20ul filter tiprack\nOpentrons 1000ul filter tiprack\nMicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plates\nEppendorf 96 Deep Well Block 1000ul\n\n\n\nDeck Setup\n Opentrons 1000ul filter tiprack (Slot 4)\n Opentrons 20ul filter tiprack (Slot 7)\n Eppendorf 96 Deep Well Block 1000ul (Slot 2)\n MicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plate (Slot 3, should be rested on top of the Eppendorf cooling block)", "internal": "3db190", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3db190/README.json b/protoBuilds/3db190/README.json index be301f923..55c41ae04 100644 --- a/protoBuilds/3db190/README.json +++ b/protoBuilds/3db190/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol automates certain steps of the Lyra Direct SARS-CoV Assay. These steps include the addition of process buffer to the deep well block, mixing of the deep well block, and transferring samples to the PCR plate. \n\n\n\nP20 multi-channel GEN2 electronic pipette\nP300 multi-channel GEN2 electronic pipette\nOpentrons 20ul filter tiprack\nOpentrons 200ul filter tiprack\nMicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plates\nEppendorf 96 Deep Well Block 1000ul\nOpentrons 10 Tube Rack with Falcon 4x50 mL, 6x15 mL Conical\nNEST 12 Well Reservoir 15 mL\n\n\n\nSingle Channel Setup:\n* Pipettes: P1000 Single GEN2 AND P20 Single GEN2\n* Opentrons 1000ul filter/standard tipracks\n* Opentrons 20ul filter/standard tipracks \n* Opentrons 10 Tube Rack with Falcon 4x50 mL, 6x15 mL Conical (Slot 1, Process Buffer in A1)\n* Eppendorf 96 Deep Well Block 1000ul (Slot 2)\n* MicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plate (Slot 3, should be rested on top of the Eppendorf cooling block)\nMulti Channel Setup:\n* Pipettes: P300 Multi GEN2 AND P20 Multi GEN2\n* Opentrons 200ul/300ul filter/standard tiprack\n* Opentrons 20ul filter/standard tiprack\n* NEST 12 Well Reservoir 15 mL (10 mL of Process Buffer in Channels 1-4)\n* Eppendorf 96 Deep Well Block 1000ul (Slot 2)\n* MicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plate (Slot 3, should be rested on top of the Eppendorf cooling block)", + "description": "This protocol automates certain steps of the Lyra Direct SARS-CoV Assay. These steps include the addition of process buffer to the deep well block, mixing of the deep well block, and transferring samples to the PCR plate. \n\n\n\nP20 multi-channel GEN2 electronic pipette\nP300 multi-channel GEN2 electronic pipette\nOpentrons 20ul filter tiprack\nOpentrons 200ul filter tiprack\nMicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plates\nEppendorf 96 Deep Well Block 1000ul\nOpentrons 10 Tube Rack with Falcon 4x50 mL, 6x15 mL Conical\nNEST 12 Well Reservoir 15 mL\n\n\n\nSingle Channel Setup:\n Pipettes: P1000 Single GEN2 AND P20 Single GEN2\n Opentrons 1000ul filter/standard tipracks\n Opentrons 20ul filter/standard tipracks \n Opentrons 10 Tube Rack with Falcon 4x50 mL, 6x15 mL Conical (Slot 1, Process Buffer in A1)\n Eppendorf 96 Deep Well Block 1000ul (Slot 2)\n MicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plate (Slot 3, should be rested on top of the Eppendorf cooling block)\nMulti Channel Setup:\n Pipettes: P300 Multi GEN2 AND P20 Multi GEN2\n Opentrons 200ul/300ul filter/standard tiprack\n Opentrons 20ul filter/standard tiprack\n NEST 12 Well Reservoir 15 mL (10 mL of Process Buffer in Channels 1-4)\n Eppendorf 96 Deep Well Block 1000ul (Slot 2)\n MicroAmp\u2122 EnduraPlate\u2122 Optical 96-Well PCR Plate (Slot 3, should be rested on top of the Eppendorf cooling block)", "internal": "3db190", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3e0bef/README.json b/protoBuilds/3e0bef/README.json index 30add863f..aa4ac776f 100644 --- a/protoBuilds/3e0bef/README.json +++ b/protoBuilds/3e0bef/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates the Omega Bio-Tek Mag-Bind\u00ae Plant DNA DS 96 Kit on the OT-2.\nUsing the P300 8-Channel Pipette, GEN2 all liquid handling steps outlined in the protocol are handled on the OT-2, with minimal user intervention. To optimize liquid handling on the automated platform, some reagents should be combined prior to adding to the deck (more details below).\nExplanation of complex parameters below:\n* Pipette Mount: Select which mount (left or right) the P300 8-Channel Pipette, GEN2 is attached to.\n* Number of Samples: Specify the number of samples (1-96). Please note ~ because the 8-channel pipette is used in this protocol, any number will be rounded up to 8.\n* Binding Time (minutes): Specify the number of minutes for binding, prior to the first supernatant removal. Please note that this is an estimate, as there will be continuous mixing throughout this step.\n* MagDeck Incubation (minutes): Specify the number of minutes to delay the robot, while the MagDeck is engaged.\n* Air Dry Time (minutes): Specify the number of minutes for air drying after the final wash step.\n* Add Water Before Air Dry: Specify whether or not to add, then remove 100\u00b5L of water immediately before the air dry step.\n* Labware for Samples Input: Select the labware that will contain the samples from the drop down.\n* [QIAGEN ONLY] Aspiration Height: Specify the height (in mm) from the bead to aspirate from (3mm is the default)\n* Final Wash Removal (in \u00b5L): Specify the volume for the supernatant removal step during the final wash.\n* Elution Volume (in \u00b5L): The volume of Elution Buffer added to each well. Please note ~ the written protocol states 100-200\u00b5L and this protocol has been designed accordingly.\n* Perform Resuspension Off-Deck: Specify whether to perform resuspension with manual intervention (Yes) or with the OT-2 Pipette (No). This will apply to the initial 10 minute incubation and the 4 wash steps.\n* Play Custom Music at Pause: Specify whether or not to play custom music during pause steps. Please note, selecting 'No' will result in the pre-installed music playing. Please only select 'Yes' if you've worked with the Opentrons team on this protocol prior to download\n\nNote: This protocol was last updated on October 27th, 2022\n", + "description": "This protocol automates the Omega Bio-Tek Mag-Bind\u00ae Plant DNA DS 96 Kit on the OT-2.\nUsing the P300 8-Channel Pipette, GEN2 all liquid handling steps outlined in the protocol are handled on the OT-2, with minimal user intervention. To optimize liquid handling on the automated platform, some reagents should be combined prior to adding to the deck (more details below).\nExplanation of complex parameters below:\n Pipette Mount: Select which mount (left or right) the P300 8-Channel Pipette, GEN2 is attached to.\n Number of Samples: Specify the number of samples (1-96). Please note ~ because the 8-channel pipette is used in this protocol, any number will be rounded up to 8.\n Binding Time (minutes): Specify the number of minutes for binding, prior to the first supernatant removal. Please note that this is an estimate, as there will be continuous mixing throughout this step.\n MagDeck Incubation (minutes): Specify the number of minutes to delay the robot, while the MagDeck is engaged.\n Air Dry Time (minutes): Specify the number of minutes for air drying after the final wash step.\n Add Water Before Air Dry: Specify whether or not to add, then remove 100\u00b5L of water immediately before the air dry step.\n Labware for Samples Input: Select the labware that will contain the samples from the drop down.\n [QIAGEN ONLY] Aspiration Height: Specify the height (in mm) from the bead to aspirate from (3mm is the default)\n Final Wash Removal (in \u00b5L): Specify the volume for the supernatant removal step during the final wash.\n Elution Volume (in \u00b5L): The volume of Elution Buffer added to each well. Please note ~ the written protocol states 100-200\u00b5L and this protocol has been designed accordingly.\n Perform Resuspension Off-Deck: Specify whether to perform resuspension with manual intervention (Yes) or with the OT-2 Pipette (No). This will apply to the initial 10 minute incubation and the 4 wash steps.\n Play Custom Music at Pause: Specify whether or not to play custom music during pause steps. Please note, selecting 'No' will result in the pre-installed music playing. Please only select 'Yes' if you've worked with the Opentrons team on this protocol prior to download\n\nNote: This protocol was last updated on October 27th, 2022\n", "internal": "3e0b3f", "labware": "\nSample Input Labware (specified in parameters)\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nNEST 96-Well PCR Plate\nNEST 96-Well Deepwell Plate, 2mL\nOpentrons 200\u00b5L Filter Tip Racks\n", "markdown": { @@ -32,7 +32,7 @@ "pipettes": "\nP300 8-Channel Pipette, GEN2\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\n[Off-robot manual step] The protocol begins with the manual addition of 720\u00b5L of CSPL Buffer + Proteinase K (700+20) to each sample.\nAfter initial incubation is complete, user can manually transfer 500\u00b5L of starting material to deepwell plate and place on Mag Deck or (if using Qiagen tubes) place empty deepwell plate on Mag Deck and samples onto OT-2 deck for automated transfer.\nIf automating the initial sample transfer, 500\u00b5L will be transferred to the 96-Well deepwell plate. Otherwise, OT-2 steps will begin with step 4.\n525\u00b5L of RNase A + RBB Buffer + Mag-Bind Beads (5+500+20) is transferred to each column containing samples.\nA 10 minute incubation period will begin. During this period, the OT-2 will mix each column for ~30 seconds before moving to the next column. In the case of 1 column of samples, the OT-2 will mix for ~30 seconds, then stop for 30 seconds before resuming the mix again.\nAfter incubating, the Mag Deck engages, and after the pellet forms, 1080\u00b5L is transferred to the NEST 1-Well Reservoir for liquid waste.\n500\u00b5L of CSPW1 Buffer is added to each column of samples and mixed.\nAfter incubating on the Mag Deck, 600\u00b5L is transferred to the liquid waste.\n500\u00b5L of CSPW2 Buffer is added to each column of samples and mixed.\nAfter incubating on the Mag Deck, 600\u00b5L is transferred to the liquid waste.\n500\u00b5L of SPM Buffer (wash 1) is added to each column of samples and mixed.\nAfter incubating on the Mag Deck, 600\u00b5L is transferred to the liquid waste.\n500\u00b5L of SPM Buffer (wash 2) is added to each column of samples and mixed.\nAfter incubating on the Mag Deck, the final wash removal volume stated is transferred to the liquid waste.\n[Optional] If the user selects to \"add water before air dry\", the pipette will slowly aspirate and dispense 100\u00b5L of nuclease-free water to each column of samples.\nA 10 minute incubation begins, at which point, the user should fill the reagent reservoir with the warmed Elution Buffer.\nOnce the incubation period is over, the Elution Buffer is added to the samples on the Mag Deck.\nThe user is prompted to remove the Plate on the Mag Deck and incubate at 65C.\nOnce the incubation is complete, the user returns the Plate to the Mag Deck.\nThe Mag Deck engages and after the pellet forms, the elution is transferred to the PCR plate.\n", - "reagent-setup": "Reagents for this protocol are split between two NEST 12-Well Reservoir, 15mL. For each reagent, a section of 2-6 channels are dedicated and when transferring to samples, channels are used sequentially. For example, the CSPW2 Buffer can be split across 4 channels. In this example, each channel can hold enough reagent for up to 3 columns of samples (24 total samples). Continuing with this example, if 32 samples were being processed, enough reagent for 3 columns of sample would fill the first dedicated channel for the CSPW2 Buffer and enough reagent for 1 column would fill the second channel.\n\nWhen determining the amount of reagent, the number of sample columns should be multiplied by eight, 1.1 (an additional 10%), and the amount of reagent needed. Based on the number of channels dedicated to each reagent, the amount needed in each channel can be calculated.\n\nThe SPM buffer is used for two, sequential washes and the protocol has been updated to utilize the columns of the reservoir sequentially (as opposed to broken into \"wash 1\" and \"wash 2\"). Given this, each column of the reservoir can hold enough reagent for 1.5 columns in the sample plate (ie, washes 1 & 2 for column 1 and wash 1 for column 2). Continuing with our example of 32 samples (4 sample columns), the first three reservoir columns would need to have SPM buffer to accomplish the protocol (see below):\n* Reservoir Well 1: Wash 1 Sample Column 1, Wash 2 Sample Column 1, Wash 1 Sample Column 2\n* Reservoir Well 2: Wash 2 Sample Column 2, Wash 1 Sample Column 3, Wash 2 Sample Column 3\n* Reservoir Well 3: Wash 1 Sample Column 4, Wash 2 Sample Column 4\n\n\nReservoir 1: Deck Slot 2\n* RNase A (5\u00b5L) + RBB Buffer (500\u00b5L) + Mag-Bind Beads (20\u00b5L): Channels 1-4\n* CSPW1 Buffer (500\u00b5L): Channels 5-8\n* CSPW2 Buffer (500\u00b5L): Channels 9-12\n\n\n\n\n\nReservoir 2: Deck Slot 3\n* SPM Buffer (500\u00b5L, x2): Channels 1-8\n* Nuclease-Free Water (if using): Channel 9\n* Elution Buffer: Channels 11 (for samples 1-48) and 12 (for samples 49-96)\n\n\n\n", + "reagent-setup": "Reagents for this protocol are split between two NEST 12-Well Reservoir, 15mL. For each reagent, a section of 2-6 channels are dedicated and when transferring to samples, channels are used sequentially. For example, the CSPW2 Buffer can be split across 4 channels. In this example, each channel can hold enough reagent for up to 3 columns of samples (24 total samples). Continuing with this example, if 32 samples were being processed, enough reagent for 3 columns of sample would fill the first dedicated channel for the CSPW2 Buffer and enough reagent for 1 column would fill the second channel.\n\nWhen determining the amount of reagent, the number of sample columns should be multiplied by eight, 1.1 (an additional 10%), and the amount of reagent needed. Based on the number of channels dedicated to each reagent, the amount needed in each channel can be calculated.\n\nThe SPM buffer is used for two, sequential washes and the protocol has been updated to utilize the columns of the reservoir sequentially (as opposed to broken into \"wash 1\" and \"wash 2\"). Given this, each column of the reservoir can hold enough reagent for 1.5 columns in the sample plate (ie, washes 1 & 2 for column 1 and wash 1 for column 2). Continuing with our example of 32 samples (4 sample columns), the first three reservoir columns would need to have SPM buffer to accomplish the protocol (see below):\n Reservoir Well 1: Wash 1 Sample Column 1, Wash 2 Sample Column 1, Wash 1 Sample Column 2\n Reservoir Well 2: Wash 2 Sample Column 2, Wash 1 Sample Column 3, Wash 2 Sample Column 3\n Reservoir Well 3: Wash 1 Sample Column 4, Wash 2 Sample Column 4\n\n\nReservoir 1: Deck Slot 2\n RNase A (5\u00b5L) + RBB Buffer (500\u00b5L) + Mag-Bind Beads (20\u00b5L): Channels 1-4\n CSPW1 Buffer (500\u00b5L): Channels 5-8\n CSPW2 Buffer (500\u00b5L): Channels 9-12\n\n\n\n\n\nReservoir 2: Deck Slot 3\n SPM Buffer (500\u00b5L, x2): Channels 1-8\n Nuclease-Free Water (if using): Channel 9\n* Elution Buffer: Channels 11 (for samples 1-48) and 12 (for samples 49-96)\n\n\n\n", "reagents": [ "Omega Bio-Tek Mag-Bind\u00ae Plant DNA DS 96 Kit" ], diff --git a/protoBuilds/3e3c9d-protocol-Adding-BTM/README.json b/protoBuilds/3e3c9d-protocol-Adding-BTM/README.json index 1cf8175f1..6955edd6c 100644 --- a/protoBuilds/3e3c9d-protocol-Adding-BTM/README.json +++ b/protoBuilds/3e3c9d-protocol-Adding-BTM/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons Corning 96 Well Plate 360 \u00b5L Flat\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nReagents\n\n\n\nSlot 1: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 2: Corning 96 Well Plate 360 \u00b5L Flat\nSlot 4: Opentrons 96 Tip-Rack 300ul\nP300-Multi Mount: Left Mount\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify number of samples in well plate.\n* Starting Tip Column: Specify which column of tips to begin drawing from.", + "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons Corning 96 Well Plate 360 \u00b5L Flat\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nReagents\n\n\n\nSlot 1: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 2: Corning 96 Well Plate 360 \u00b5L Flat\nSlot 4: Opentrons 96 Tip-Rack 300ul\nP300-Multi Mount: Left Mount\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify number of samples in well plate.\n Starting Tip Column: Specify which column of tips to begin drawing from.", "internal": "3e3c9d-protocol-Adding-BTM", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3e3c9d-protocol-Adding-Water-RBC/README.json b/protoBuilds/3e3c9d-protocol-Adding-Water-RBC/README.json index 174acaa80..a81bb2ac1 100644 --- a/protoBuilds/3e3c9d-protocol-Adding-Water-RBC/README.json +++ b/protoBuilds/3e3c9d-protocol-Adding-Water-RBC/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons Corning 96 Well Plate 360 \u00b5L Flat\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nReagents\n\n\n\nSlot 1: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 2: Corning 96 Well Plate 360 \u00b5L Flat\nSlot 4: Opentrons 96 Tip-Rack 300ul\nP300-Multi Mount: Left\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify number of samples in well plate.\n* Starting Tip Column: Specify which column of tips to begin drawing from.", + "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons Corning 96 Well Plate 360 \u00b5L Flat\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nReagents\n\n\n\nSlot 1: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 2: Corning 96 Well Plate 360 \u00b5L Flat\nSlot 4: Opentrons 96 Tip-Rack 300ul\nP300-Multi Mount: Left\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify number of samples in well plate.\n Starting Tip Column: Specify which column of tips to begin drawing from.", "internal": "3e3c9d-protocol-Adding-Water-RBC", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3e3c9d-protocol-master-rbc-transfer/README.json b/protoBuilds/3e3c9d-protocol-master-rbc-transfer/README.json index 3610a6bff..e327689f3 100644 --- a/protoBuilds/3e3c9d-protocol-master-rbc-transfer/README.json +++ b/protoBuilds/3e3c9d-protocol-master-rbc-transfer/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Single-Channel Pipette\nOpentrons P50 Multi-Channel Pipette\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nOmegaquant 96-Well Plate\nBlood Tube Rack\n200ul Tip-Rack and Tips\nReagents\n\n\n\nSlot 2: Omegaquant 96-Well Plate\nSlot 3: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 4: Opentrons 96 Tip-Rack 300ul\nSlot 5: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 6: 200ul Tip-Rack\nSlot 7: Blood Tube Rack\nSlot 8: Blood Tube Rack\nSlot 10: Blood Tube Rack\nSlot 11: Blood Tube Rack\nP300-Multi Mount: Left\nP50-Single Mount: Right\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify number of samples in well plate.\n* Starting Tip Column: Specify which column of tips to begin drawing from.", + "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Single-Channel Pipette\nOpentrons P50 Multi-Channel Pipette\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nOmegaquant 96-Well Plate\nBlood Tube Rack\n200ul Tip-Rack and Tips\nReagents\n\n\n\nSlot 2: Omegaquant 96-Well Plate\nSlot 3: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 4: Opentrons 96 Tip-Rack 300ul\nSlot 5: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 6: 200ul Tip-Rack\nSlot 7: Blood Tube Rack\nSlot 8: Blood Tube Rack\nSlot 10: Blood Tube Rack\nSlot 11: Blood Tube Rack\nP300-Multi Mount: Left\nP50-Single Mount: Right\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify number of samples in well plate.\n Starting Tip Column: Specify which column of tips to begin drawing from.", "internal": "3e3c9d-protocol-Master-RBC-Transfer", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3e3c9d-protocols-adding-wistd-water/README.json b/protoBuilds/3e3c9d-protocols-adding-wistd-water/README.json index 768ecf36e..64cdd55a0 100644 --- a/protoBuilds/3e3c9d-protocols-adding-wistd-water/README.json +++ b/protoBuilds/3e3c9d-protocols-adding-wistd-water/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons Corning 96 Well Plate 360 \u00b5L Flat\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nReagents\n\n\n\nSlot 2: Corning 96 Well Plate 360 \u00b5L Flat\nSlot 4: Opentrons 96 Tip-Rack 300ul\nSlot 5: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 9: Electron Microscopy Sciences Rectangular Staining Dish\nP300-Multi Mount: Left\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify number of samples in well plate.\n* Starting Tip Column: Specify which column of tips to begin drawing from.", + "description": "This protocol updates an existing protocol request from Opentrons API Version 1 to Opentrons API Version 2.\n\nUsing the customizable parameters below, you can specify which column to start picking up tips from and how many samples are in each run for each protocol. \n\nThis protocol uses custom labware definitions for the glass trough (Electron Microscopy Sciences), Omegaquant 96-Well Plate, Blood Tube Rack, and 200ul Tip Rack. When downloading the protocol, the labware definitions (a JSON file) will be included for use with this protocol. For more information on using custom labware on the OT-2, please see this article: Using labware in your protocols\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P50 Multi-Channel Pipette\nOpentrons Corning 96 Well Plate 360 \u00b5L Flat\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nElectron Microscopy Sciences Rectangular Staining Dish [https://www.emsdiasum.com/microscopy/products/histology/staining.aspx#70314]\nReagents\n\n\n\nSlot 2: Corning 96 Well Plate 360 \u00b5L Flat\nSlot 4: Opentrons 96 Tip-Rack 300ul\nSlot 5: Electron Microscopy Sciences Rectangular Staining Dish\nSlot 9: Electron Microscopy Sciences Rectangular Staining Dish\nP300-Multi Mount: Left\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify number of samples in well plate.\n Starting Tip Column: Specify which column of tips to begin drawing from.", "internal": "3e3c9d-protocols-Adding-WISTD-Water", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3fad82-part-2/README.json b/protoBuilds/3fad82-part-2/README.json index 5b1bb7a59..6945776fc 100644 --- a/protoBuilds/3fad82-part-2/README.json +++ b/protoBuilds/3fad82-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons p20 tips (Deck Slots 2,3,5)\nOpentrons p300 tips (Deck Slot 6)\nOpentrons Thermocycler Module (Deck Slots 7,8,10,11)\nOpentrons Magnetic Module with Sample Plate (Deck Slot 4)\nReagent Reservoir (Deck Slot 1)\n", - "description": "Part 2 of 3: Clean Up and PCR Enrichment.\nLinks:\n* Part 1: End Prep and Adapter Ligation\n* Part 2: Clean Up and PCR Enrichment\n* Part 3: Final Clean Up\nWith this protocol, your robot can perform a modified Quarter Volume NEBNext Ultra II FS DNA Library Prep Kit for Illumina protocol described by the Experimental Protocol. NEB Instruction Manual for NEBNext.\nThis is part 2 of the protocol: Clean up and PCR enrichment.\nThis protocol assumes up to 96 input samples and follows the attached experimental protocol.\nAfter the steps carried out in this protocol (part 2), proceed with part 3: Final Clean Up.", + "description": "Part 2 of 3: Clean Up and PCR Enrichment.\nLinks:\n Part 1: End Prep and Adapter Ligation\n Part 2: Clean Up and PCR Enrichment\n* Part 3: Final Clean Up\nWith this protocol, your robot can perform a modified Quarter Volume NEBNext Ultra II FS DNA Library Prep Kit for Illumina protocol described by the Experimental Protocol. NEB Instruction Manual for NEBNext.\nThis is part 2 of the protocol: Clean up and PCR enrichment.\nThis protocol assumes up to 96 input samples and follows the attached experimental protocol.\nAfter the steps carried out in this protocol (part 2), proceed with part 3: Final Clean Up.", "internal": "3fad82-part-2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3fad82-part-3/README.json b/protoBuilds/3fad82-part-3/README.json index d7d4a9602..2b54a6fa1 100644 --- a/protoBuilds/3fad82-part-3/README.json +++ b/protoBuilds/3fad82-part-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons p20 tips (Deck Slots 2,3)\nOpentrons p300 tips (Deck Slots 5,6)\nOpentrons Thermocycler Module-deactivated (Deck Slots 7,8,10,11)\nOpentrons Magnetic Module with Sample Plate (Deck Slot 4)\nReagent Reservoir (Deck Slot 1)\n", - "description": "Part 3 of 3: Final Clean Up.\nLinks:\n* Part 1: End Prep and Adapter Ligation\n* Part 2: Clean Up and PCR Enrichment\n* Part 3: Final Clean Up\nWith this protocol, your robot can perform a modified Quarter Volume NEBNext Ultra II FS DNA Library Prep Kit for Illumina protocol described by the Experimental Protocol. NEB Instruction Manual for NEBNext.\nThis is part 3 of the protocol: Final Clean Up.\nThis protocol assumes up to 96 input samples and follows the attached experimental protocol.", + "description": "Part 3 of 3: Final Clean Up.\nLinks:\n Part 1: End Prep and Adapter Ligation\n Part 2: Clean Up and PCR Enrichment\n* Part 3: Final Clean Up\nWith this protocol, your robot can perform a modified Quarter Volume NEBNext Ultra II FS DNA Library Prep Kit for Illumina protocol described by the Experimental Protocol. NEB Instruction Manual for NEBNext.\nThis is part 3 of the protocol: Final Clean Up.\nThis protocol assumes up to 96 input samples and follows the attached experimental protocol.", "internal": "3fad82-part-3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/3fad82/README.json b/protoBuilds/3fad82/README.json index a62ab0f21..5616d9dac 100644 --- a/protoBuilds/3fad82/README.json +++ b/protoBuilds/3fad82/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons p20 tips (Deck Slots 2,3,5,6)\nOpentrons Thermocycler Module (Deck Slots 7,8,10,11)\nMaster Mix Plate (Deck Slot 4)\n", - "description": "Part 1 of 3: End Prep and Adapter Ligation.\nLinks:\n* Part 1: End Prep and Adapter Ligation\n* Part 2: Clean Up and PCR Enrichment\n* Part 3: Final Clean Up\nWith this protocol, your robot can perform a modified Quarter Volume NEBNext Ultra II FS DNA Library Prep Kit for Illumina protocol described by the Experimental Protocol. NEB Instruction Manual for NEBNext.\nThis is part 1 of the protocol: End prep and adapter ligation.\nThis protocol assumes up to 96 input samples and follows the attached experimental protocol.\nAfter the steps carried out in this protocol (part 1), proceed with part 2: Clean Up and PCR Enrichment.", + "description": "Part 1 of 3: End Prep and Adapter Ligation.\nLinks:\n Part 1: End Prep and Adapter Ligation\n Part 2: Clean Up and PCR Enrichment\n* Part 3: Final Clean Up\nWith this protocol, your robot can perform a modified Quarter Volume NEBNext Ultra II FS DNA Library Prep Kit for Illumina protocol described by the Experimental Protocol. NEB Instruction Manual for NEBNext.\nThis is part 1 of the protocol: End prep and adapter ligation.\nThis protocol assumes up to 96 input samples and follows the attached experimental protocol.\nAfter the steps carried out in this protocol (part 1), proceed with part 2: Clean Up and PCR Enrichment.", "internal": "3fad82", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/400b8e/README.json b/protoBuilds/400b8e/README.json index 27c767104..d0d6a67ed 100644 --- a/protoBuilds/400b8e/README.json +++ b/protoBuilds/400b8e/README.json @@ -5,7 +5,7 @@ "Cherrypicking" ] }, - "description": "\nCherrypicking, or hit-picking, is a key component of many workflows from high-throughput screening to microbial transfections. With this protocol, you can easily select specific wells in any labware without worrying about missing or selecting the wrong well. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol. You will be prompted to interact with the deck during pauses if necessary throughout the protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nMicroplates (96-well or 384-well)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nLabware will be loaded automatically by specifying the labware loadname and labware slot in the .csv file. All available empty slots will be filled with the necessary tipracks, and the user will be prompted to refill the tipracks if all are emptied in the middle of the protocol. To pause mid-protocol to replenish source plates on the deck, add a line in the .csv that reads pause (see example below for a deeper explanation).\nCSV Format\nYour cherrypicking transfers must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). Note that the header line (first row of the .csv file) should also be included!\nHere's an example of how a short cherrypicking protocol should be properly formatted:\nSource Labware ID,Source Labware Type,Source Slot,Source Well,Source Aspiration Height Above Bottom (in mm),Dest Labware Type,Dest Slot,Dest Well,Volume (in ul)\nRNA1,agilent_1_reservoir_290ml,3,A1,1,nest_96_wellplate_100ul_pcr_full_skirt,4,A11,1\nRNA2,nest_12_reservoir_15ml,4,A1,1,nest_96_wellplate_2ml_deep,5,A5,3\npause,,,,,,,,\nRNA3,nest_1_reservoir_195ml,5,A1,1,nest_96_wellplate_2ml_deep,5,H12,7\nIn this example, 1\u03bcL will be transferred from 1mm above the bottom of well A1 in an Agilent 1-well 290ml reservoir (slot 1) to well A11 in the destination NEST 96-well plate 100\u00b5l (slot 4). After this, 3\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 12-well 15ml reservoir (slot 2) to well A5 in the destination NEST 96-well plate 100\u00b5l (slot 5). Last, 7\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 1-well 195ml reservoir (slot 3) to well H12 in the destination NEST 96-well plate 100\u00b5l (slot 5).\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV for use with this protocol.\nUsing the customizations fields, below set up your protocol.\n* Transfer .csv File: Upload the .csv file containing your well locations, volumes, and source plate (optional).\n* Pipette Model: Select which pipette you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n* Tip Type: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", + "description": "\nCherrypicking, or hit-picking, is a key component of many workflows from high-throughput screening to microbial transfections. With this protocol, you can easily select specific wells in any labware without worrying about missing or selecting the wrong well. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol. You will be prompted to interact with the deck during pauses if necessary throughout the protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nMicroplates (96-well or 384-well)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nLabware will be loaded automatically by specifying the labware loadname and labware slot in the .csv file. All available empty slots will be filled with the necessary tipracks, and the user will be prompted to refill the tipracks if all are emptied in the middle of the protocol. To pause mid-protocol to replenish source plates on the deck, add a line in the .csv that reads pause (see example below for a deeper explanation).\nCSV Format\nYour cherrypicking transfers must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). Note that the header line (first row of the .csv file) should also be included!\nHere's an example of how a short cherrypicking protocol should be properly formatted:\nSource Labware ID,Source Labware Type,Source Slot,Source Well,Source Aspiration Height Above Bottom (in mm),Dest Labware Type,Dest Slot,Dest Well,Volume (in ul)\nRNA1,agilent_1_reservoir_290ml,3,A1,1,nest_96_wellplate_100ul_pcr_full_skirt,4,A11,1\nRNA2,nest_12_reservoir_15ml,4,A1,1,nest_96_wellplate_2ml_deep,5,A5,3\npause,,,,,,,,\nRNA3,nest_1_reservoir_195ml,5,A1,1,nest_96_wellplate_2ml_deep,5,H12,7\nIn this example, 1\u03bcL will be transferred from 1mm above the bottom of well A1 in an Agilent 1-well 290ml reservoir (slot 1) to well A11 in the destination NEST 96-well plate 100\u00b5l (slot 4). After this, 3\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 12-well 15ml reservoir (slot 2) to well A5 in the destination NEST 96-well plate 100\u00b5l (slot 5). Last, 7\u03bcL will be transferred from 1mm above the bottom of well A1 in a NEST 1-well 195ml reservoir (slot 3) to well H12 in the destination NEST 96-well plate 100\u00b5l (slot 5).\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV for use with this protocol.\nUsing the customizations fields, below set up your protocol.\n Transfer .csv File: Upload the .csv file containing your well locations, volumes, and source plate (optional).\n Pipette Model: Select which pipette you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n Tip Type: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", "internal": "400b8e", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/407d5e/README.json b/protoBuilds/407d5e/README.json index aeb032354..fe9a59579 100644 --- a/protoBuilds/407d5e/README.json +++ b/protoBuilds/407d5e/README.json @@ -5,7 +5,7 @@ "Assay" ] }, - "description": "This workflow is comprised of a protein labelling protocol that begins by adding several reagents to samples and then incubating at 37C for several days (up to 4) and aliquoting 20\u00b5L of the incubating samples. For more information about this protocol, including materials needed and customizable parameters, please see below before downloading.\n\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons Temperature Module with Aluminum Blocks\nP300 Single-Channel Pipette\nP20 Single-Channel Pipette\nOpentrons 300\u00b5l Pipette Tips\nOpentrons 20\u00b5L Pipette Tips\nNEST 96-Well PCR Plates\nNEST 1.5mL Microcentrifuge Tubes & Tubes for Samples\nReagents\nSamples\n\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples (1-19): Specify the number of samples to run (1-19).\n* Number of Incubations: Specify the number of incubations. The protocol will transfer 20\u00b5L to the destination plate and repeat the process, up to three times, at the 1, 2, and 4 day mark.\n* Labware Containing Samples: Select the type of tube that will be used to contain the samples. This tube should be place in the 24-Well Aluminum Block.\n* Temperature Module: Select which generation of the Temperature Module will be used.\n* Reset Tipracks?: This protocol can save the state of the tipracks after each run for the P300 and the P20. If this is set to \"Yes\" (or the protocol is run for the first time on the robot), the protocol will begin picking up tips from the A1 of Tiprack 1 for each pipette. If set to \"No\", the saved tip state from the previous run will be accessed and the pipette will begin using tips where the previous protocol run left off. The user will be prompted to replace the corresponding tip racks.\n\n\nDeck Layout\n\nSlot 1: Destination Plate (NEST 96-Well PCR Plates) - 20\u00b5L of sample aliquots will be transferred here. This should be replaced for transfer after incubation(s).\n\nSlot 2: 24-Well Aluminum Block containing Tubes (specified by user) with Samples\n\nSlot 3: Opentrons 20\u00b5L Tiprack (Tiprack 3)\n\nSlot 4: Opentrons Temperature Module with 96-Well Aluminum Block and NEST 96-Well PCR Plates\n\nSlot 5: NEST 96-Well PCR Plates (Empty, for mixing)\n\nSlot 6: Opentrons 20\u00b5L Tiprack (Tiprack 2)\n\nSlot 7: 24-Well Aluminum Block containing 1.5mL NEST Tubes with Reagents\n\nSlot 8: Opentrons 300\u00b5L Tiprack (Tiprack 1)\n\nSlot 9: Opentrons 20\u00b5L Tiprack (Tiprack 1)\n\nSlot 10: Opentrons 300\u00b5L Tiprack (Tiprack 3)\n\nSlot 11: Opentrons 300\u00b5L Tiprack (Tiprack 2)\n", + "description": "This workflow is comprised of a protein labelling protocol that begins by adding several reagents to samples and then incubating at 37C for several days (up to 4) and aliquoting 20\u00b5L of the incubating samples. For more information about this protocol, including materials needed and customizable parameters, please see below before downloading.\n\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons Temperature Module with Aluminum Blocks\nP300 Single-Channel Pipette\nP20 Single-Channel Pipette\nOpentrons 300\u00b5l Pipette Tips\nOpentrons 20\u00b5L Pipette Tips\nNEST 96-Well PCR Plates\nNEST 1.5mL Microcentrifuge Tubes & Tubes for Samples\nReagents\nSamples\n\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples (1-19): Specify the number of samples to run (1-19).\n Number of Incubations: Specify the number of incubations. The protocol will transfer 20\u00b5L to the destination plate and repeat the process, up to three times, at the 1, 2, and 4 day mark.\n Labware Containing Samples: Select the type of tube that will be used to contain the samples. This tube should be place in the 24-Well Aluminum Block.\n Temperature Module: Select which generation of the Temperature Module will be used.\n* Reset Tipracks?: This protocol can save the state of the tipracks after each run for the P300 and the P20. If this is set to \"Yes\" (or the protocol is run for the first time on the robot), the protocol will begin picking up tips from the A1 of Tiprack 1 for each pipette. If set to \"No\", the saved tip state from the previous run will be accessed and the pipette will begin using tips where the previous protocol run left off. The user will be prompted to replace the corresponding tip racks.\n\n\nDeck Layout\n\nSlot 1: Destination Plate (NEST 96-Well PCR Plates) - 20\u00b5L of sample aliquots will be transferred here. This should be replaced for transfer after incubation(s).\n\nSlot 2: 24-Well Aluminum Block containing Tubes (specified by user) with Samples\n\nSlot 3: Opentrons 20\u00b5L Tiprack (Tiprack 3)\n\nSlot 4: Opentrons Temperature Module with 96-Well Aluminum Block and NEST 96-Well PCR Plates\n\nSlot 5: NEST 96-Well PCR Plates (Empty, for mixing)\n\nSlot 6: Opentrons 20\u00b5L Tiprack (Tiprack 2)\n\nSlot 7: 24-Well Aluminum Block containing 1.5mL NEST Tubes with Reagents\n\nSlot 8: Opentrons 300\u00b5L Tiprack (Tiprack 1)\n\nSlot 9: Opentrons 20\u00b5L Tiprack (Tiprack 1)\n\nSlot 10: Opentrons 300\u00b5L Tiprack (Tiprack 3)\n\nSlot 11: Opentrons 300\u00b5L Tiprack (Tiprack 2)\n", "internal": "407d5e", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", diff --git a/protoBuilds/4175de/README.json b/protoBuilds/4175de/README.json index d2a8bccf9..c09859561 100644 --- a/protoBuilds/4175de/README.json +++ b/protoBuilds/4175de/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol performs a custom cherrypicked PCR/qPRC prep. It requires a CSV input for the source and destination wells of the samples. It will automatically add mastermix based on the number of samples inputted to the PCR plate sequentially (A1-12 then B1-12, etc...).\n\n\nOpentrons Temperature Module\nP20 single-channel GEN2 electronic pipette\nOpentrons 20ul filter tiprack\nCorning 96-Well Nonbinding Surface Microplates (3641)\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 24 Tube Rack with Generic 2 mL Screwcap\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\n\n\n\nDeck Setup\n* Opentrons 20ul filter tiprack (Slot 1, Slot 4, Slot 7)\n* Opentrons 24 Tube Rack with Generic 2 mL Screwcap (Slot 2, Mastermix in well A6)\n* Opentrons Temperature Module (Slot 3)\n* 96 well PCR Strip (Aluminum Block) OR 96 well NEST 100uL PCR Plate (Slot 3 on Temperature Module)\n* Corning 96-Well Nonbinding Surface Microplates OR Opentrons 24-slot Tube Rack (Slot 5, Slot 6, Slot 8, Slot 11)", + "description": "This protocol performs a custom cherrypicked PCR/qPRC prep. It requires a CSV input for the source and destination wells of the samples. It will automatically add mastermix based on the number of samples inputted to the PCR plate sequentially (A1-12 then B1-12, etc...).\n\n\nOpentrons Temperature Module\nP20 single-channel GEN2 electronic pipette\nOpentrons 20ul filter tiprack\nCorning 96-Well Nonbinding Surface Microplates (3641)\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 24 Tube Rack with Generic 2 mL Screwcap\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\n\n\n\nDeck Setup\n Opentrons 20ul filter tiprack (Slot 1, Slot 4, Slot 7)\n Opentrons 24 Tube Rack with Generic 2 mL Screwcap (Slot 2, Mastermix in well A6)\n Opentrons Temperature Module (Slot 3)\n 96 well PCR Strip (Aluminum Block) OR 96 well NEST 100uL PCR Plate (Slot 3 on Temperature Module)\n* Corning 96-Well Nonbinding Surface Microplates OR Opentrons 24-slot Tube Rack (Slot 5, Slot 6, Slot 8, Slot 11)", "internal": "4175de", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/422b1e/README.json b/protoBuilds/422b1e/README.json index 382caf6ae..a55c35e56 100644 --- a/protoBuilds/422b1e/README.json +++ b/protoBuilds/422b1e/README.json @@ -5,7 +5,7 @@ "Custom Titration" ] }, - "description": "This titration protocol utilizes a custom labware definition (beaker + stir plate) for use on the OT-2.\nThe P1000 Pipette (attached to the right mount) will pick up a tip from the tip rack located in slot 11. For each tube in the Opentrons Tube Rack (located in slot 9), the pipette will transfer 2mL to the beaker in slot 4, wait a predetermined amount of time, then transfer 2mL from the beaker in slot 4 to the beaker in slot 8.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P1000 Single-Channel Pipette\nOpentrons 1000\u00b5L Tips\nOpentrons 4-in-1 Tube Rack Set, 6x50mL Top\n50mL Conical Tubes\nCustom Beaker + Stir Plate\nReagents\n\n\n\nSlot 4: Custom Beaker + Stir Plate\nSlot 8: Custom Beaker + Stir Plate (Waste Container)\nSlot 9: Opentrons 4-in-1 Tube Rack Set, 6x50mL Top with 50mL Conical Tubes containing reagents*\n* The P1000 will aspirate liquid from the bottom of the tube, so do not overfill the tube to ensure the pipette does not submerge itself in liquid.\nSlot 11: Opentrons 1000\u00b5L Tips", + "description": "This titration protocol utilizes a custom labware definition (beaker + stir plate) for use on the OT-2.\nThe P1000 Pipette (attached to the right mount) will pick up a tip from the tip rack located in slot 11. For each tube in the Opentrons Tube Rack (located in slot 9), the pipette will transfer 2mL to the beaker in slot 4, wait a predetermined amount of time, then transfer 2mL from the beaker in slot 4 to the beaker in slot 8.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P1000 Single-Channel Pipette\nOpentrons 1000\u00b5L Tips\nOpentrons 4-in-1 Tube Rack Set, 6x50mL Top\n50mL Conical Tubes\nCustom Beaker + Stir Plate\nReagents\n\n\n\nSlot 4: Custom Beaker + Stir Plate\nSlot 8: Custom Beaker + Stir Plate (Waste Container)\nSlot 9: Opentrons 4-in-1 Tube Rack Set, 6x50mL Top with 50mL Conical Tubes containing reagents\n The P1000 will aspirate liquid from the bottom of the tube, so do not overfill the tube to ensure the pipette does not submerge itself in liquid.\nSlot 11: Opentrons 1000\u00b5L Tips", "internal": "422b1e", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/42d27b/README.json b/protoBuilds/42d27b/README.json index 207a0353f..f423e93f7 100644 --- a/protoBuilds/42d27b/README.json +++ b/protoBuilds/42d27b/README.json @@ -5,7 +5,7 @@ "Quant-iT dsDNA Kit" ] }, - "description": "This protocol automates the steps outlined in the Quant-iT dsDNA Broad-Range Assay Kit. Using a P10 Multi-Channel Pipette and a P300 Multi-Channel Pipette, this protocol adds reagent mix (buffer + dye) to 96-well plate, before adding 1\u00b5L of DNA from sample tubes.\nUsing the customizations fields, below set up your protocol.\n* P300 Multi Mount: Select which mount (left or right) the P300 Multi is attached to.\n* P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Multi-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 10\u00b5L Tips\nOpentrons 300\u00b5L Tips\nNEST 12-Well Reservoir, 15mL\nAxygen 96-Well Plate (PCR-96-FS-C)\nMicronics 96-Tubes in Plate (MP52757S-Y20)\nReagents\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n* A1: Reagent Mix\nSlot 2: Axygen 96-Well Plate (PCR-96-FS-C)\nSlot 3: Micronics 96-Tubes in Plate (MP52757S-Y20)\nSlot 4: Opentrons 300\u00b5L Tips\nSlot 5: Opentrons 10\u00b5L Tips", + "description": "This protocol automates the steps outlined in the Quant-iT dsDNA Broad-Range Assay Kit. Using a P10 Multi-Channel Pipette and a P300 Multi-Channel Pipette, this protocol adds reagent mix (buffer + dye) to 96-well plate, before adding 1\u00b5L of DNA from sample tubes.\nUsing the customizations fields, below set up your protocol.\n P300 Multi Mount: Select which mount (left or right) the P300 Multi is attached to.\n P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Multi-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 10\u00b5L Tips\nOpentrons 300\u00b5L Tips\nNEST 12-Well Reservoir, 15mL\nAxygen 96-Well Plate (PCR-96-FS-C)\nMicronics 96-Tubes in Plate (MP52757S-Y20)\nReagents\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n* A1: Reagent Mix\nSlot 2: Axygen 96-Well Plate (PCR-96-FS-C)\nSlot 3: Micronics 96-Tubes in Plate (MP52757S-Y20)\nSlot 4: Opentrons 300\u00b5L Tips\nSlot 5: Opentrons 10\u00b5L Tips", "internal": "42d27b", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/441cc8/README.json b/protoBuilds/441cc8/README.json index 3f54a94f6..94e521f1f 100644 --- a/protoBuilds/441cc8/README.json +++ b/protoBuilds/441cc8/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol uses a p300 multi-channel pipette to suspend a column of indexing primers (contained in a 96-well PCR plate) in master mix (contained in a reagent reservoir) and then distributes 14 ul of this mixture to the corresponding column of each of 9 PCR plates (in order as shown in the attached deck map). This process is repeated for all columns of the primer plate to fill all columns of the 9 PCR plates.\nThe liquid handling method used for the master mix includes the following features:\nslow flow rate for aspiration and dispense\nwait for liquid to finish moving after aspiration and dispense\navoid introducing air into liquid (avoid complete dispenses)\ndispense to a surface\nwithdraw tip slowly from liquid\nLinks:\n* Deck Layout\n* Process Steps\nWith this protocol, your robot can prepare stock plates containing master mix and indexing primers to be used for the indexing step of an NGS library prep workflow.", + "description": "This protocol uses a p300 multi-channel pipette to suspend a column of indexing primers (contained in a 96-well PCR plate) in master mix (contained in a reagent reservoir) and then distributes 14 ul of this mixture to the corresponding column of each of 9 PCR plates (in order as shown in the attached deck map). This process is repeated for all columns of the primer plate to fill all columns of the 9 PCR plates.\nThe liquid handling method used for the master mix includes the following features:\nslow flow rate for aspiration and dispense\nwait for liquid to finish moving after aspiration and dispense\navoid introducing air into liquid (avoid complete dispenses)\ndispense to a surface\nwithdraw tip slowly from liquid\nLinks:\n Deck Layout\n Process Steps\nWith this protocol, your robot can prepare stock plates containing master mix and indexing primers to be used for the indexing step of an NGS library prep workflow.", "internal": "441cc8", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4471ba/README.json b/protoBuilds/4471ba/README.json index 126b3eba2..f6f1a7704 100644 --- a/protoBuilds/4471ba/README.json +++ b/protoBuilds/4471ba/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol automates filling plates that have been turned 90-degrees on the deck. Using custom adapters, the P300 Multi-Channel Pipette is used to transfer a set volume (selected below) from a Beckman Coulter 8-Channel Reservoir to a Simport 96-Well Plate (on an adapter that allows the plate to be turned 90-degrees). The P300 Multi-Channel pipette picks up tips from an Opentrons Tip Rack (also on an adapter), by picking up 8/12 tips from the column (liquid transfer happens to 8/12 wells in column on plates) and then the last 4 tips in the column (for last 4/12 wells in columns on plates).\n\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons P300 Multi-Channel Pipette (GEN2)\nOpentrons 300\u00b5L Tip Rack\n(2x) Simport 96-Well Plate, 1200\u00b5L\nBeckman Coulter 8-Channel Reservoir, 19mL\nReagents\n\n\n\nDeck Layout\n\nSlot 2/5: Simport 96-Well Plate, in adapter (Plate 1)\n\nSlot 8/11: Simport 96-Well Plate, in adapter (Plate 1)\n\nSlot 4/7: Opentrons 300\u00b5L Tip Rack (in adapter)\n\nSlot 10: Beckman Coulter 8-Channel Reservoir with Reagents\n\n\nUsing the customizations field (below), set up your protocol.\n* P300-Multi Mount: Select which mount (left or right) the P300-Multi is attached to.\n* Transfer Volume (\u00b5L): Specify the volume (in \u00b5L) that should be transferred to each well.\n* Number of Columns to Fill (1-8): Specify the number of columns to fill in each plate.", + "description": "This protocol automates filling plates that have been turned 90-degrees on the deck. Using custom adapters, the P300 Multi-Channel Pipette is used to transfer a set volume (selected below) from a Beckman Coulter 8-Channel Reservoir to a Simport 96-Well Plate (on an adapter that allows the plate to be turned 90-degrees). The P300 Multi-Channel pipette picks up tips from an Opentrons Tip Rack (also on an adapter), by picking up 8/12 tips from the column (liquid transfer happens to 8/12 wells in column on plates) and then the last 4 tips in the column (for last 4/12 wells in columns on plates).\n\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons P300 Multi-Channel Pipette (GEN2)\nOpentrons 300\u00b5L Tip Rack\n(2x) Simport 96-Well Plate, 1200\u00b5L\nBeckman Coulter 8-Channel Reservoir, 19mL\nReagents\n\n\n\nDeck Layout\n\nSlot 2/5: Simport 96-Well Plate, in adapter (Plate 1)\n\nSlot 8/11: Simport 96-Well Plate, in adapter (Plate 1)\n\nSlot 4/7: Opentrons 300\u00b5L Tip Rack (in adapter)\n\nSlot 10: Beckman Coulter 8-Channel Reservoir with Reagents\n\n\nUsing the customizations field (below), set up your protocol.\n P300-Multi Mount: Select which mount (left or right) the P300-Multi is attached to.\n Transfer Volume (\u00b5L): Specify the volume (in \u00b5L) that should be transferred to each well.\n* Number of Columns to Fill (1-8): Specify the number of columns to fill in each plate.", "internal": "4471ba", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/44981c/README.json b/protoBuilds/44981c/README.json index ccee9bcee..a1db5a3c9 100644 --- a/protoBuilds/44981c/README.json +++ b/protoBuilds/44981c/README.json @@ -5,7 +5,7 @@ "Cherrypicking" ] }, - "description": "This protocol performs cherrypicking from source to target plates as specified in an input CSV file. The protocol parses the CSV for slots to load the source and target plates. Only non-zero volume transfers are carried out for efficiency, and the user is prompted to refill tipracks if necessary.\n\nThis protocol is an update of this APIv1 protocol.\n\nYou will need:\n* P10 Single-channel electronic pipette\n* P50 Single-channel electronic pipette\n* P300 Single-channel electronic pipette\n* 10\u00b5l Pipette tips\n* 300\u00b5l Pipette tips\n* Biorad Hard-Shell 96-Well PCR Plates # HSP9601\n* Opentrons 4-in-1 Tube Rack Set", + "description": "This protocol performs cherrypicking from source to target plates as specified in an input CSV file. The protocol parses the CSV for slots to load the source and target plates. Only non-zero volume transfers are carried out for efficiency, and the user is prompted to refill tipracks if necessary.\n\nThis protocol is an update of this APIv1 protocol.\n\nYou will need:\n P10 Single-channel electronic pipette\n P50 Single-channel electronic pipette\n P300 Single-channel electronic pipette\n 10\u00b5l Pipette tips\n 300\u00b5l Pipette tips\n Biorad Hard-Shell 96-Well PCR Plates # HSP9601\n* Opentrons 4-in-1 Tube Rack Set", "internal": "44981c", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", diff --git a/protoBuilds/44b1ac/README.json b/protoBuilds/44b1ac/README.json index 636639f3f..90e3be1be 100644 --- a/protoBuilds/44b1ac/README.json +++ b/protoBuilds/44b1ac/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nIf the deck layout of a particular protocol is more or less static, it is often helpful to attach a preview of the deck layout, most descriptively generated with Labware Creator. Example:\n\n", - "description": "This protocol automates the QIAseq Targeted RNAscan Panel for Illumina Instruments protocol in the QIAseq Targeted RNAscan Panel on the OT-2. The QIAseq Targeted RNAscan Panels are a complete Sample to Insight solution that applies the molecular barcode-based digital RNA sequencing strategy to quantify known and new fusion genes.\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* Samples Labware Type: The starting samples can be placed in either 1.5 mL tubes on the Opentrons Tube Rack OR in a 96 Well Plate.\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* IL-N7 Adapter Row: Choose the row the adapters will be used from either Plates A, B, C, or D.\n* Magnetic Module Engage Height: The height the magnets will raise on the magnetic module.\n* Wash 1 Bead Volume: Choose the bead volume based on RNA quality.\n* Wash 2 Bead Volume: Choose the bead volume based on RNA quality (This value is used for all subsequent bead washes). \n", + "description": "This protocol automates the QIAseq Targeted RNAscan Panel for Illumina Instruments protocol in the QIAseq Targeted RNAscan Panel on the OT-2. The QIAseq Targeted RNAscan Panels are a complete Sample to Insight solution that applies the molecular barcode-based digital RNA sequencing strategy to quantify known and new fusion genes.\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n Samples Labware Type: The starting samples can be placed in either 1.5 mL tubes on the Opentrons Tube Rack OR in a 96 Well Plate.\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n IL-N7 Adapter Row: Choose the row the adapters will be used from either Plates A, B, C, or D.\n Magnetic Module Engage Height: The height the magnets will raise on the magnetic module.\n Wash 1 Bead Volume: Choose the bead volume based on RNA quality.\n Wash 2 Bead Volume: Choose the bead volume based on RNA quality (This value is used for all subsequent bead washes). \n", "internal": "44b1ac", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nNEST 2 mL 96-Well Deep Well Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/453b5a/README.json b/protoBuilds/453b5a/README.json index 86ba847ce..12fbac096 100644 --- a/protoBuilds/453b5a/README.json +++ b/protoBuilds/453b5a/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol performs a custom nucleic acid purification and PCR preparation on a PCR plate mounted on an Opentrons temperature module with aluminum block insert. The final step of the protocol is to transfer various PCR mixes in 1.5ml tubes to corresponding tubes. The source mix tubes and destination wells in the PCR plate should be specified in .csv format as in the following example:\nmix tube,PCR plate start well,PCR plate end well\nA1,A1,H2\nB1,A3,H6\nC1,A7,H8\nD1,A9,H12\nYou can also download a template for this input here, edit in a spreadsheet editor like Google Sheets, MS Excel, or Apple Numbers, export as a .csv file, and upload below as the .csv file to specify PCR mix destinations parameter.\nThe user is prompted to refill tipracks when necessary for both the P20 single-channel and P300 multi-channel pipettes.\n\n\n\nOpentrons temperature module with 96-well aluminum block insert holding Biozym 96-well PCR plate #712547 200\u00b5l\nCustom 24-cuvette racks for Greiner Bio-One Vacuette tubes (1-4)\nOpentrons 4-in-1 tuberack with 4x6 insert for Eppendorf 1.5 mL Safe-Lock Snapcap tubes\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nOpentrons P20 single-channel GEN2 electronic pipette\nOpentrons P300 multi-channel electronic pipette\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\nblood collection tube racks (slots 7, 8, 10, 11):\n* tubes 1-24: slot 7\n* tubes 25-48: slot 8\n* tubes 49-72: slot 10\n* tubes 73-96: slot 11\n12-channel reservoir (slot 1)\n* channel 1: concentration dilution\n* channel 2: buffer B\n* channels 3-5: buffer C\n* channels 9-12: liquid waste (loaded empty)", + "description": "This protocol performs a custom nucleic acid purification and PCR preparation on a PCR plate mounted on an Opentrons temperature module with aluminum block insert. The final step of the protocol is to transfer various PCR mixes in 1.5ml tubes to corresponding tubes. The source mix tubes and destination wells in the PCR plate should be specified in .csv format as in the following example:\nmix tube,PCR plate start well,PCR plate end well\nA1,A1,H2\nB1,A3,H6\nC1,A7,H8\nD1,A9,H12\nYou can also download a template for this input here, edit in a spreadsheet editor like Google Sheets, MS Excel, or Apple Numbers, export as a .csv file, and upload below as the .csv file to specify PCR mix destinations parameter.\nThe user is prompted to refill tipracks when necessary for both the P20 single-channel and P300 multi-channel pipettes.\n\n\n\nOpentrons temperature module with 96-well aluminum block insert holding Biozym 96-well PCR plate #712547 200\u00b5l\nCustom 24-cuvette racks for Greiner Bio-One Vacuette tubes (1-4)\nOpentrons 4-in-1 tuberack with 4x6 insert for Eppendorf 1.5 mL Safe-Lock Snapcap tubes\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nOpentrons P20 single-channel GEN2 electronic pipette\nOpentrons P300 multi-channel electronic pipette\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\nblood collection tube racks (slots 7, 8, 10, 11):\n tubes 1-24: slot 7\n tubes 25-48: slot 8\n tubes 49-72: slot 10\n tubes 73-96: slot 11\n12-channel reservoir (slot 1)\n channel 1: concentration dilution\n channel 2: buffer B\n channels 3-5: buffer C\n channels 9-12: liquid waste (loaded empty)", "internal": "453b5a", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/459a55/README.json b/protoBuilds/459a55/README.json index 8d9c4cad4..28f492635 100644 --- a/protoBuilds/459a55/README.json +++ b/protoBuilds/459a55/README.json @@ -5,7 +5,7 @@ "Mass Spec" ] }, - "description": "This protocol performs a custom mass spec sample prep for up to 20 samples.\n\n\n\nOpentrons temperature module with NEST 96-well PCR plate 100\u00b5l full skirt\n4x6 aluminum block for NEST 1.5ml snapcap tubes\nOpentrons 20\u00b5l tiprack\nOpentrons 300\u00b5l tiprack\nOpentrons P20 and P300 GEN2 single-channel electronic pipette\n\n\n\n4x6 aluminum block for NEST 1.5ml snapcap tubes (slot 2)\n* tube D1: denaturing solution\n* tube D2: DTT\n* all other tubes: samples that will be transferred to their corresponding locations in sample plate", + "description": "This protocol performs a custom mass spec sample prep for up to 20 samples.\n\n\n\nOpentrons temperature module with NEST 96-well PCR plate 100\u00b5l full skirt\n4x6 aluminum block for NEST 1.5ml snapcap tubes\nOpentrons 20\u00b5l tiprack\nOpentrons 300\u00b5l tiprack\nOpentrons P20 and P300 GEN2 single-channel electronic pipette\n\n\n\n4x6 aluminum block for NEST 1.5ml snapcap tubes (slot 2)\n tube D1: denaturing solution\n tube D2: DTT\n* all other tubes: samples that will be transferred to their corresponding locations in sample plate", "internal": "459a55", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/45a320/README.json b/protoBuilds/45a320/README.json index fc902adc8..d980c3d56 100644 --- a/protoBuilds/45a320/README.json +++ b/protoBuilds/45a320/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOn slot 2, empty tubes should be placed in every other column starting from column 1 (e.g. columns 1, 3, 5), which the protocol refers to when it pauses and prompts the user for instruction. Columns 2, 4, and 6 will be the binding column columns of the tube rack. Please see protocol steps below.\n\n", - "description": "This protocol extracts DNA using the ReliaPrep\u2122 Viral TNA Miniprep System extraction kit. Proteinase K, patient sample, cell lysis buffer and isopropanol are combined with a ReliaPrep Binding Column. After 3 washes, water is added to the column to form the eluate which can then be plated. \nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples for this run. Samples should always be placed by column (A1, B1, C1,..,etc.).\n* P20/P1000 Dispense Flow Rate: Global control of P20 and P1000 dispense flow rate. A value of 1.0 is default, 0.5 is 50% of the default flow rate, 1.2 is 20% faster the default flow rate, etc.\n* P20 Mount: Specify which side (left or right) to mount the P20 single channel pipette.\n* P1000 Mount: Specify which side (left or right) to mount the P1000 single channel pipette.\n", + "description": "This protocol extracts DNA using the ReliaPrep\u2122 Viral TNA Miniprep System extraction kit. Proteinase K, patient sample, cell lysis buffer and isopropanol are combined with a ReliaPrep Binding Column. After 3 washes, water is added to the column to form the eluate which can then be plated. \nExplanation of complex parameters below:\n Number of samples: Specify the number of samples for this run. Samples should always be placed by column (A1, B1, C1,..,etc.).\n P20/P1000 Dispense Flow Rate: Global control of P20 and P1000 dispense flow rate. A value of 1.0 is default, 0.5 is 50% of the default flow rate, 1.2 is 20% faster the default flow rate, etc.\n P20 Mount: Specify which side (left or right) to mount the P20 single channel pipette.\n P1000 Mount: Specify which side (left or right) to mount the P1000 single channel pipette.\n", "internal": "45a320", "labware": "\nOpentrons 4-in-1 Tube Rack Set\nOpentrons 1000ul Tips\nOpentrons 20ul Tips\nVacutainer tubes\n1.5mL tubes\n", "markdown": { diff --git a/protoBuilds/470d8c/README.json b/protoBuilds/470d8c/README.json index 11bf5fd51..f3188373f 100644 --- a/protoBuilds/470d8c/README.json +++ b/protoBuilds/470d8c/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol automates the steps of transferring mastermix from source plates to destination plates. It also automates the transfer of template to destination plates.\n\n\n\nP300 multi-channel GEN2 electronic pipette\nP20 multi-channel GEN2 electronic pipette\nOpentrons 300ul tiprack\nOpentrons 20ul tiprack\nThermo Scientific\u2122 PCR Plate, 96-well, semi-skirted\nEppendorf PCR cooler\n\n\n\nDeck Setup\n* Source Plate (PCR Plate on top of Eppendorf Cooler) (Slot 1)\n* Opentrons 20 uL tip rack (Slot 7, 10, 11)\n* Opentrons 300 uL tip rack (Slot 4)\n* Template Plates (PCR Plate on top of Eppendorf Cooler) (Slots 2, 5, 8)\n* Destination Plates (PCR Plate on top of Eppendorf Cooler) (Slots 3, 6, 9)\nRobot map:\n| Tips P20 | Tips P20 | Waste |\n| Tips P20 | Template Plate #1 | Dest Plate #1 |\n| Tips P300 | Template Plate #2 | Dest Plate #2 |\n| Source Plate #1 | Template Plate #3 | Dest Plate #3 | ", + "description": "This protocol automates the steps of transferring mastermix from source plates to destination plates. It also automates the transfer of template to destination plates.\n\n\n\nP300 multi-channel GEN2 electronic pipette\nP20 multi-channel GEN2 electronic pipette\nOpentrons 300ul tiprack\nOpentrons 20ul tiprack\nThermo Scientific\u2122 PCR Plate, 96-well, semi-skirted\nEppendorf PCR cooler\n\n\n\nDeck Setup\n Source Plate (PCR Plate on top of Eppendorf Cooler) (Slot 1)\n Opentrons 20 uL tip rack (Slot 7, 10, 11)\n Opentrons 300 uL tip rack (Slot 4)\n Template Plates (PCR Plate on top of Eppendorf Cooler) (Slots 2, 5, 8)\n* Destination Plates (PCR Plate on top of Eppendorf Cooler) (Slots 3, 6, 9)\nRobot map:\n| Tips P20 | Tips P20 | Waste |\n| Tips P20 | Template Plate #1 | Dest Plate #1 |\n| Tips P300 | Template Plate #2 | Dest Plate #2 |\n| Source Plate #1 | Template Plate #3 | Dest Plate #3 | ", "internal": "470d8c", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/49b828/README.json b/protoBuilds/49b828/README.json index 670745de9..e556569f0 100644 --- a/protoBuilds/49b828/README.json +++ b/protoBuilds/49b828/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: Samples will be dispensed per plate to the 384 well plate by column. Column 1 plate 1 --> A1 of 384, column 2 plate 1 --> B1, column 3 plate 1 --> A2 so on and so forth. Each plate is then 6 columns of the 384 well plate. If there is an unfilled column (i.e. 54 samples = 0.5 plates + 6 samples), then the protocol will use 8 tips up to column 6 of the 96 well plate, pick up 6 tips, then go to dispense into A7 of the 384 well plate. For a full run (382 samples), mastermix will be supplied to all wells. For all other sample numbers, mastermix will not be provided to O24 and P24, and will have to be put in manually. Do not run this protocol for 368 < sample number < 384 samples.\n\n\n", - "description": "This protocol preps a 384 well plate with mastermix and sample. Plates should loaded in order of slots 7, 8, 1, and 2. See below for how plates are transferred to the 384 well plate. If running a full run (382 samples), mastermix will be provided to the wells O24 and P24. If not running a full run, mastermix and controls will have to be placed manually. H11 and H12 of the final plate on slot 2 should be left empty if running a full run.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples in this run. Samples 1-96 will go in plate 1 slot 7, samples 97-192 will go in plate 2 slot 8, samples 193-288 will go in plate 3 slot 1, samples 289-384 will go in plate 4 slot 2. Samples will be put into the 384 well plate in the following manner:\n* 96 Well Plate Type: Specify whether using the four 96 plates as the Kingfisher plate (depth 12.8mm) or the thermofisher plate (depth 42.3mm).\n* 384 Well Plate Type: Specify whether using the 384 plate with the clear numbers, or the 384 plate with the black numbers. Plate should be mounted on aluminum block.\n* Use Temperature Module?: Specify whether using the temperature module or not on the 384 plate in slot 3 for this run. The temperature module will be set at 4C. If not using the temperature module, just place the 384 plate in slot 3 with no aluminum block.\n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 Single-Channel pipette.\n", + "description": "This protocol preps a 384 well plate with mastermix and sample. Plates should loaded in order of slots 7, 8, 1, and 2. See below for how plates are transferred to the 384 well plate. If running a full run (382 samples), mastermix will be provided to the wells O24 and P24. If not running a full run, mastermix and controls will have to be placed manually. H11 and H12 of the final plate on slot 2 should be left empty if running a full run.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples in this run. Samples 1-96 will go in plate 1 slot 7, samples 97-192 will go in plate 2 slot 8, samples 193-288 will go in plate 3 slot 1, samples 289-384 will go in plate 4 slot 2. Samples will be put into the 384 well plate in the following manner:\n 96 Well Plate Type: Specify whether using the four 96 plates as the Kingfisher plate (depth 12.8mm) or the thermofisher plate (depth 42.3mm).\n 384 Well Plate Type: Specify whether using the 384 plate with the clear numbers, or the 384 plate with the black numbers. Plate should be mounted on aluminum block.\n Use Temperature Module?: Specify whether using the temperature module or not on the 384 plate in slot 3 for this run. The temperature module will be set at 4C. If not using the temperature module, just place the 384 plate in slot 3 with no aluminum block.\n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 Single-Channel pipette.\n", "internal": "49b828", "labware": "\nOpentrons 20ul Filter Tips\nNEST 12 well 15mL Reservoir\nThermo Scientific KingFisher Flex 96 well plates\nThermo-Fisher 384 well microplate\n", "markdown": { diff --git a/protoBuilds/49de51-pt1/README.json b/protoBuilds/49de51-pt1/README.json index 3a96a2876..0498adf47 100644 --- a/protoBuilds/49de51-pt1/README.json +++ b/protoBuilds/49de51-pt1/README.json @@ -5,7 +5,7 @@ "Plant DNA" ] }, - "description": "This protocol automates the ThermoFischer MagMAX Plant DNA Isolation Kit on up to 192 samples (2 plates of 96). The entire workflow is broken into 2 different protocols. This is part 1, disrupting the tissue.\n\nIn this protocol, 590\u00b5L of buffer (combination of 500\u00b5L lysis Buffer A, 70\u00b5L of Lysis Buffer B, and 20\u00b5L of RNase A) is added to each well. The user is then prompted to remove the plate(s) for off deck vortexing/shaking and incubation. Once incubation is complete, the user returns the plate(s) to the deck and the robot will add 130\u00b5L of the precipitation solution. After one final incubation off the robot and a spin down, 400\u00b5L of supernatant is transferred to a deep well plate. The 400\u00b5L sample can be stored or purified with part 2 of the protocol.\n\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons p300 Multi-Channel Pipette (attached to right mount)\nOpentrons 200\u00b5L Filter Tip Rack\nNEST 1-Well Reservoir, 195mL\nNEST 12-Well Reservoir, 15mL\n96-Deep Well Plate (such as the OMNI 96-Well Deep Well Plate with Ceramic Beads)\nMagMAX\u2122 Plant DNA Isolation Kit\nSamples\n\n\n\nDeck Layout\n\nSlot 1: NEST 12-Well Reservoir, 15mL\n* A1: Precipitation Solution, 13.5mL (for Plate 1)\n* A2: Precipitation Solution, 13.5mL (for Plate 2)\nSlot 2: OMNI 96-Well Deep Well Plate with Ceramic Beads containing sample (Plate 1)\n\nSlot 3: NEST 96-Well Deep Well Plate (empty, for Plate 1 supernatant)\n\nSlot 4: NEST 1-Well Reservoir, 195mL\nFor each plate, the following should be added:\n* Lysis Buffer A, 52mL\n* Lysis Buffer B, 4.160mL\n* RNase A, 2.080mL\nSlot 5: OMNI 96-Well Deep Well Plate with Ceramic Beads containing sample (Plate 2)\n\nSlot 6: NEST 96-Well Deep Well Plate (empty, for Plate 2 supernatant)\n\nSlot 7: Opentrons 200\u00b5L Filter Tip Rack\n\nSlot 10: Opentrons 200\u00b5L Filter Tip Rack\n\nSlot 11: Opentrons 200\u00b5L Filter Tip Rack\n", + "description": "This protocol automates the ThermoFischer MagMAX Plant DNA Isolation Kit on up to 192 samples (2 plates of 96). The entire workflow is broken into 2 different protocols. This is part 1, disrupting the tissue.\n\nIn this protocol, 590\u00b5L of buffer (combination of 500\u00b5L lysis Buffer A, 70\u00b5L of Lysis Buffer B, and 20\u00b5L of RNase A) is added to each well. The user is then prompted to remove the plate(s) for off deck vortexing/shaking and incubation. Once incubation is complete, the user returns the plate(s) to the deck and the robot will add 130\u00b5L of the precipitation solution. After one final incubation off the robot and a spin down, 400\u00b5L of supernatant is transferred to a deep well plate. The 400\u00b5L sample can be stored or purified with part 2 of the protocol.\n\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons p300 Multi-Channel Pipette (attached to right mount)\nOpentrons 200\u00b5L Filter Tip Rack\nNEST 1-Well Reservoir, 195mL\nNEST 12-Well Reservoir, 15mL\n96-Deep Well Plate (such as the OMNI 96-Well Deep Well Plate with Ceramic Beads)\nMagMAX\u2122 Plant DNA Isolation Kit\nSamples\n\n\n\nDeck Layout\n\nSlot 1: NEST 12-Well Reservoir, 15mL\n A1: Precipitation Solution, 13.5mL (for Plate 1)\n A2: Precipitation Solution, 13.5mL (for Plate 2)\nSlot 2: OMNI 96-Well Deep Well Plate with Ceramic Beads containing sample (Plate 1)\n\nSlot 3: NEST 96-Well Deep Well Plate (empty, for Plate 1 supernatant)\n\nSlot 4: NEST 1-Well Reservoir, 195mL\nFor each plate, the following should be added:\n Lysis Buffer A, 52mL\n Lysis Buffer B, 4.160mL\n* RNase A, 2.080mL\nSlot 5: OMNI 96-Well Deep Well Plate with Ceramic Beads containing sample (Plate 2)\n\nSlot 6: NEST 96-Well Deep Well Plate (empty, for Plate 2 supernatant)\n\nSlot 7: Opentrons 200\u00b5L Filter Tip Rack\n\nSlot 10: Opentrons 200\u00b5L Filter Tip Rack\n\nSlot 11: Opentrons 200\u00b5L Filter Tip Rack\n", "internal": "49de51-pt1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/49de51-pt2/README.json b/protoBuilds/49de51-pt2/README.json index 037b52ea4..4e5be1789 100644 --- a/protoBuilds/49de51-pt2/README.json +++ b/protoBuilds/49de51-pt2/README.json @@ -5,7 +5,7 @@ "Plant DNA" ] }, - "description": "This protocol automates the ThermoFischer MagMAX Plant DNA Isolation Kit on up to 96 samples. The entire workflow is broken into 2 different protocols. This is part 2, DNA purification.\n\nIn this protocol, 25\u00b5L of magnetic beads plus 400\u00b5L of ethanol is added to 400\u00b5L of sample (from part 1). After off-deck mixing, the plate is returned to the OT-2 for supernatant removal. This process continues with wash buffer 1, wash buffer 2, and the elution buffer. However, the supernatant of the elution buffer is preserved in a 96-well PCR plate and can be used for further downstream application.\n\n\nUpdate April 26, 2021: The addition of magnetic beads has been made optional.\n\nUpdate May 3, 2021: A second wash step has been added and heights of aspiration adjusted.\n\nUpdate June 8, 2021: Added the ability to park tips. This will cut down on tip usage when using 48+ samples.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons Magnetic Module, GEN2\nOpentrons p300 Multi-Channel Pipette (attached to right mount)\nOpentrons 200\u00b5L Filter Tip Rack\nNEST 1-Well Reservoir, 195mL\nNEST 12-Well Reservoir, 15mL\nNEST 96-Well Deep Well Plate\nNEST 96-Well PCR Plate\nMagMAX\u2122 Plant DNA Isolation Kit\nSamples\n\n\n\nDeck Layout\n\nSlot 11: NEST 1-Well Reservoir, 195mL (for liquid waste)\n\nSlot 4: NEST 12-Well Reservoir, 15mL\n* A1: Magnetic Beads (see note 1 below)\n* A2: Ethanol (Samples 1-32)\n* A3: Ethanol (Samples 33-64)\n* A4: Ethanol (Samples 65-96)\n* A5: empty\n* A6: empty\n* A7: empty\n* A8: empty\n* A9: empty\n* A10: Wash Buffer 1 (Samples 1-32)\n* A11: Wash Buffer 1 (Samples 33-64)\n* A12: Wash Buffer 1 (Samples 65-96)\nSlot 5: NEST 12-Well Reservoir, 15mL\n* A1: Wash Buffer 2 (Samples 1-32)\n* A2: Wash Buffer 2 (Samples 33-64)\n* A3: Wash Buffer 2 (Samples 65-96)\n* A4: Wash Buffer 2 (Samples 1-32)\n* A5: Wash Buffer 2 (Samples 33-64)\n* A6: Wash Buffer 2 (Samples 65-96)\n* A7: empty\n* A8: empty\n* A9: empty\n* A10: empty\n* A11: Elution Buffer (Samples 1-48)\n* A12: Elution Buffer (Samples 49-96)\nSlot 10: Labware Containing Magnetic Beads (see note 1 below)\n\nSlot 7: Opentrons Magnetic Module, GEN2 with NEST 96-Well Deep Well Plate containing Samples\n\nSlot 1: NEST 96-Well PCR Plate\n\nSlot 8: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\nSlot 9: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\nSlot 6: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\nSlot 3: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\n\nSlot 2: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\n\nNote 1: If using, the Magnetic Beads can be placed in well 1 of the NEST 12-Well Reservoir (in slot 4) or in column 1 of a different piece of labware (in slot 10)\nNote 2: Ten (10) columns of tips are needed per column of sample and will be accessed in the following order: slot 8, 9, 6, 3, 2. In the case that more than 48 samples are used, the user will be prompted midway through the protocol to replace the tips.\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: specify the number of samples (1-96)\n* Deep Well Plate Type: select the type of deep well plate used (holding samples)\n* Automate Bead Addition: select whether or not to automate the addition of magnetic beads\n* Location of Magnetic Beads: select the location of the magnetic beads (labware; deck slot: well)\n* Park Tips: Select Yes or No. If Yes is selected, one tiprack (in slot 2) will be used for all mixing and supernatant removals; the other tips should be placed in slot 3 and 6.\n\n", + "description": "This protocol automates the ThermoFischer MagMAX Plant DNA Isolation Kit on up to 96 samples. The entire workflow is broken into 2 different protocols. This is part 2, DNA purification.\n\nIn this protocol, 25\u00b5L of magnetic beads plus 400\u00b5L of ethanol is added to 400\u00b5L of sample (from part 1). After off-deck mixing, the plate is returned to the OT-2 for supernatant removal. This process continues with wash buffer 1, wash buffer 2, and the elution buffer. However, the supernatant of the elution buffer is preserved in a 96-well PCR plate and can be used for further downstream application.\n\n\nUpdate April 26, 2021: The addition of magnetic beads has been made optional.\n\nUpdate May 3, 2021: A second wash step has been added and heights of aspiration adjusted.\n\nUpdate June 8, 2021: Added the ability to park tips. This will cut down on tip usage when using 48+ samples.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.21.0 or later)\nOpentrons Magnetic Module, GEN2\nOpentrons p300 Multi-Channel Pipette (attached to right mount)\nOpentrons 200\u00b5L Filter Tip Rack\nNEST 1-Well Reservoir, 195mL\nNEST 12-Well Reservoir, 15mL\nNEST 96-Well Deep Well Plate\nNEST 96-Well PCR Plate\nMagMAX\u2122 Plant DNA Isolation Kit\nSamples\n\n\n\nDeck Layout\n\nSlot 11: NEST 1-Well Reservoir, 195mL (for liquid waste)\n\nSlot 4: NEST 12-Well Reservoir, 15mL\n A1: Magnetic Beads (see note 1 below)\n A2: Ethanol (Samples 1-32)\n A3: Ethanol (Samples 33-64)\n A4: Ethanol (Samples 65-96)\n A5: empty\n A6: empty\n A7: empty\n A8: empty\n A9: empty\n A10: Wash Buffer 1 (Samples 1-32)\n A11: Wash Buffer 1 (Samples 33-64)\n A12: Wash Buffer 1 (Samples 65-96)\nSlot 5: NEST 12-Well Reservoir, 15mL\n A1: Wash Buffer 2 (Samples 1-32)\n A2: Wash Buffer 2 (Samples 33-64)\n A3: Wash Buffer 2 (Samples 65-96)\n A4: Wash Buffer 2 (Samples 1-32)\n A5: Wash Buffer 2 (Samples 33-64)\n A6: Wash Buffer 2 (Samples 65-96)\n A7: empty\n A8: empty\n A9: empty\n A10: empty\n A11: Elution Buffer (Samples 1-48)\n A12: Elution Buffer (Samples 49-96)\nSlot 10: Labware Containing Magnetic Beads (see note 1 below)\n\nSlot 7: Opentrons Magnetic Module, GEN2 with NEST 96-Well Deep Well Plate containing Samples\n\nSlot 1: NEST 96-Well PCR Plate\n\nSlot 8: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\nSlot 9: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\nSlot 6: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\nSlot 3: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\n\nSlot 2: Opentrons 200\u00b5L Filter Tip Rack (see note 2 below)\n\n\nNote 1: If using, the Magnetic Beads can be placed in well 1 of the NEST 12-Well Reservoir (in slot 4) or in column 1 of a different piece of labware (in slot 10)\nNote 2: Ten (10) columns of tips are needed per column of sample and will be accessed in the following order: slot 8, 9, 6, 3, 2. In the case that more than 48 samples are used, the user will be prompted midway through the protocol to replace the tips.\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: specify the number of samples (1-96)\n Deep Well Plate Type: select the type of deep well plate used (holding samples)\n Automate Bead Addition: select whether or not to automate the addition of magnetic beads\n Location of Magnetic Beads: select the location of the magnetic beads (labware; deck slot: well)\n* Park Tips: Select Yes or No. If Yes is selected, one tiprack (in slot 2) will be used for all mixing and supernatant removals; the other tips should be placed in slot 3 and 6.\n\n", "internal": "49de51-pt2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4a0be6/README.json b/protoBuilds/4a0be6/README.json index 35e4cf087..bd59319b2 100644 --- a/protoBuilds/4a0be6/README.json +++ b/protoBuilds/4a0be6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: Source Labware containing reagent\nSlots 2-10: Custom Tube Racks containing Sarstedt Tubes\nSlot 11: Opentrons Tiprack\n", - "description": "This protocol is an updated version (APIv1 to APIv2) of this protocol: Tube Filling into 48-well or 24-well Tube Racks\nThis protocol allows your robot to transfer solution from a single source tube (15 mL or 50 mL Falcon conical tube) or Beckman Coulter reservoir to up to nine 48-well, 24-well, or 12-well tube racks containing Sarstedt screw-cap tubes (either 0.5 mL, 1.5 mL or 2 mL). User must specify parameters (explained below) for each run.\nExplanation of complex parameters below:\n* Transfer Volume (in \u00b5L): volume to be transferred to each Sarstedt tube\n* Tube Rack Type: tube rack format to be used to hold the Sarstedt tubes\n* Tube Type: Sarstedt tube format to be used in the protocol\n* Number of Racks: total number of Sarstedt tube racks to be filled (1-9)\n* Source Container Type: Labware containing reagent to be distributed\n* Starting Stock Volume (in mL): starting volume inside source container\n* Pipette Type: Single-channel Pipette to be used\n* Pipette Mount: the side to which you wish to attach the above pipette\n* Starting Tip: the tip to be used in the tip rack, pick from A1-H12\n* Dispense Mode: choose to either transfer (1-to-1) or distribute (1-to-many)\n* Touch Tip?: this will add an additional touch tip after dispensing liquid\n", + "description": "This protocol is an updated version (APIv1 to APIv2) of this protocol: Tube Filling into 48-well or 24-well Tube Racks\nThis protocol allows your robot to transfer solution from a single source tube (15 mL or 50 mL Falcon conical tube) or Beckman Coulter reservoir to up to nine 48-well, 24-well, or 12-well tube racks containing Sarstedt screw-cap tubes (either 0.5 mL, 1.5 mL or 2 mL). User must specify parameters (explained below) for each run.\nExplanation of complex parameters below:\n Transfer Volume (in \u00b5L): volume to be transferred to each Sarstedt tube\n Tube Rack Type: tube rack format to be used to hold the Sarstedt tubes\n Tube Type: Sarstedt tube format to be used in the protocol\n Number of Racks: total number of Sarstedt tube racks to be filled (1-9)\n Source Container Type: Labware containing reagent to be distributed\n Starting Stock Volume (in mL): starting volume inside source container\n Pipette Type: Single-channel Pipette to be used\n Pipette Mount: the side to which you wish to attach the above pipette\n Starting Tip: the tip to be used in the tip rack, pick from A1-H12\n Dispense Mode: choose to either transfer (1-to-1) or distribute (1-to-many)\n* Touch Tip?: this will add an additional touch tip after dispensing liquid\n", "internal": "4a0be6", "labware": "\nOpentrons Tiprack\nSource Labware:\n15mL Falcon Tube in Opentrons Tube Rack with 15 Tube Topper,\n50mL Falcon Tube in Opentrons Tube Rack with 6 Tube Topper,\nor Beckman Coulter Reservoir\nCustom Tube Rack with Sarstedt Tubes\n", "markdown": { diff --git a/protoBuilds/4b4a80-adapter_ligation/README.json b/protoBuilds/4b4a80-adapter_ligation/README.json index 91e5359c2..b1d67940d 100644 --- a/protoBuilds/4b4a80-adapter_ligation/README.json +++ b/protoBuilds/4b4a80-adapter_ligation/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module (Deck Slot 2)\nOpentrons p300 tips (Deck Slot 3)\nOpentrons p20 tips (Deck Slot 6)\nOpentrons Thermocycler Module (Deck Slots 7,8,10,11)\n", - "description": "Part 2 of 4: Adapter ligation and User enzyme treatment.\nLinks:\n* Part 1: Fragmentation\n* Part 2: Adapter Ligation\n* Part 3: Size Selection\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 2 of the protocol: Adapter Ligation.\nThis step performs the ligation with the NEBNext Adaptor followed by U excision.\nThis protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the ligation and user enzyme steps carried out in this protocol (part 2), samples may be held overnight at -20 C before proceeding with part 3: Size Selection. If you are stopping, seal the plate and store at -20 C.", + "description": "Part 2 of 4: Adapter ligation and User enzyme treatment.\nLinks:\n Part 1: Fragmentation\n Part 2: Adapter Ligation\n Part 3: Size Selection\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 2 of the protocol: Adapter Ligation.\nThis step performs the ligation with the NEBNext Adaptor followed by U excision.\nThis protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the ligation and user enzyme steps carried out in this protocol (part 2), samples may be held overnight at -20 C before proceeding with part 3: Size Selection. If you are stopping, seal the plate and store at -20 C.", "internal": "4b4a80-adapter_ligation", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4b4a80-fragmentation/README.json b/protoBuilds/4b4a80-fragmentation/README.json index d9e21c0c3..c249e749a 100644 --- a/protoBuilds/4b4a80-fragmentation/README.json +++ b/protoBuilds/4b4a80-fragmentation/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module (Deck Slot 2)\nOpentrons p300 tips (Deck Slot 3)\nOpentrons p20 tips (Deck Slot 6)\nOpentrons Thermocycler Module (Deck Slots 7,8,10,11)\n", - "description": "Part 1 of 4: Fragment genomic DNA and prepare ends for adapter ligation.\nLinks:\n* Part 1: Fragmentation\n* Part 2: Adapter Ligation\n* Part 3: Size Selection\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 1 of the protocol: Fragmentation.\nThis step fragments the input DNA into a tunable size range (choose optimal size range by setting the incubation time with the \"Incubation Time for Fragmentation (minutes)\" parameter below following guidelines in the instruction manual) suitable for sequencing and prepares the ends for adapter ligation. This protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the steps carried out in this protocol (part 1), it is best to immediately proceed with part 2: Adapter Ligation. If you are stopping (not recommended-a slight loss in yield may occur), seal the plate and store at -20 C.", + "description": "Part 1 of 4: Fragment genomic DNA and prepare ends for adapter ligation.\nLinks:\n Part 1: Fragmentation\n Part 2: Adapter Ligation\n Part 3: Size Selection\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 1 of the protocol: Fragmentation.\nThis step fragments the input DNA into a tunable size range (choose optimal size range by setting the incubation time with the \"Incubation Time for Fragmentation (minutes)\" parameter below following guidelines in the instruction manual) suitable for sequencing and prepares the ends for adapter ligation. This protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the steps carried out in this protocol (part 1), it is best to immediately proceed with part 2: Adapter Ligation. If you are stopping (not recommended-a slight loss in yield may occur), seal the plate and store at -20 C.", "internal": "4b4a80-fragmentation", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4b4a80-pcr_enrichment/README.json b/protoBuilds/4b4a80-pcr_enrichment/README.json index 245a5bdcc..5ec0a4747 100644 --- a/protoBuilds/4b4a80-pcr_enrichment/README.json +++ b/protoBuilds/4b4a80-pcr_enrichment/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module (Deck Slot 2)\nOpentrons p300 tips (Deck Slots 3,6,9)\nOpentrons Thermocycler Module (Deck Slots 7,8,10,11)\nOpentrons Magnetic Module (Deck Slot 4)\nReagent reservoir (Deck Slot 5)\nEluate plate (Deck Slot 1)\n", - "description": "Part 4 of 4: Enrichment, barcoding, and post-PCR clean up of size-selected DNA fragments\nLinks:\n* Part 1: Fragmentation\n* Part 2: Adapter Ligation\n* Part 3: Size Selection\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 4 of the protocol: PCR enrichment\nThis step amplifies and barcodes the size-selected output from part 3, followed by a post-PCR cleanup.\nThis protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the pcr enrichment and cleanup steps carried out in this protocol, store samples at -20 C.", + "description": "Part 4 of 4: Enrichment, barcoding, and post-PCR clean up of size-selected DNA fragments\nLinks:\n Part 1: Fragmentation\n Part 2: Adapter Ligation\n Part 3: Size Selection\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 4 of the protocol: PCR enrichment\nThis step amplifies and barcodes the size-selected output from part 3, followed by a post-PCR cleanup.\nThis protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the pcr enrichment and cleanup steps carried out in this protocol, store samples at -20 C.", "internal": "4b4a80-pcr_enrichment", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4b4a80-size_selection/README.json b/protoBuilds/4b4a80-size_selection/README.json index 048f78404..99ddfa71b 100644 --- a/protoBuilds/4b4a80-size_selection/README.json +++ b/protoBuilds/4b4a80-size_selection/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module (Deck Slot 2)\nOpentrons p300 tips (Deck Slots 6,9)\nOpentrons p20 tips (Deck Slot 3)\nOpentrons Magnetic Module (Deck Slot 4)\nReagent Reservoir (Deck Slot 5)\nSupernatant Plate (Deck Slot 7)\nEluate Plate (Deck Slot 1)\n", - "description": "Part 3 of 4: Size select and clean up the adapter-ligated and User-enzyme-treated DNA fragments (the output from Part 2).\nLinks:\n* Part 1: Fragmentation\n* Part 2: Adapter Ligation\n* Part 3: Size Selection\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 3 of the protocol: Size Selection\nThis step size-selects and cleans up the sample output from part 2 to obtain a specific insert size range of 350-600 bp. Choose pcr labware compatible with the Opentrons Magnetic Module such as \"(Magnetic Module compatible) Nest 96 wellplate 100ul pcr full skirt\" using the parameters below.\nThis protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the size selection and cleanup steps carried out in this protocol (part 3), proceed with part 4: PCR enrichment, or seal the plate and store at -20 C.", + "description": "Part 3 of 4: Size select and clean up the adapter-ligated and User-enzyme-treated DNA fragments (the output from Part 2).\nLinks:\n Part 1: Fragmentation\n Part 2: Adapter Ligation\n Part 3: Size Selection\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II FS DNA Library Prep Kit for Illumina E6177S/L protocol described by the NEBNext E6177S/L. NEB Instruction Manual for NEBNext E6177S/L.\nThis is part 3 of the protocol: Size Selection\nThis step size-selects and cleans up the sample output from part 2 to obtain a specific insert size range of 350-600 bp. Choose pcr labware compatible with the Opentrons Magnetic Module such as \"(Magnetic Module compatible) Nest 96 wellplate 100ul pcr full skirt\" using the parameters below.\nThis protocol assumes up to 24 input DNA samples of > 100 ng and follows Section 2 of the NEB Instruction Manual.\nAfter the size selection and cleanup steps carried out in this protocol (part 3), proceed with part 4: PCR enrichment, or seal the plate and store at -20 C.", "internal": "4b4a80-size_selection", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4b76c0/README.json b/protoBuilds/4b76c0/README.json index 6eba46189..4b5c03af5 100644 --- a/protoBuilds/4b76c0/README.json +++ b/protoBuilds/4b76c0/README.json @@ -5,7 +5,7 @@ "Normalization" ] }, - "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library prep. With this protocol, you can easily normalize the concentrations of samples in a 96-well Axygen plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\nUsing the customizations fields, below set up your protocol.\n* Volumes CSV: Upload the CSV (.csv) containing your diluent volumes.\n* P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Single-Channel Pipette\nOpentrons 10\u00b5L Tips\nNEST 12-Well Reservoir, 15mL\nAxygen 96-Well Plate (PCR-96-FS-C)\nDiluent\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n* A1: Diluent\nSlot 2: Axygen 96-Well Plate (PCR-96-FS-C)\nSlot 3: Opentrons 10\u00b5L Tips", + "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library prep. With this protocol, you can easily normalize the concentrations of samples in a 96-well Axygen plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\nUsing the customizations fields, below set up your protocol.\n Volumes CSV: Upload the CSV (.csv) containing your diluent volumes.\n P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P10 Single-Channel Pipette\nOpentrons 10\u00b5L Tips\nNEST 12-Well Reservoir, 15mL\nAxygen 96-Well Plate (PCR-96-FS-C)\nDiluent\nSamples\n\n\n\nSlot 1: NEST 12-Well Reservoir\n* A1: Diluent\nSlot 2: Axygen 96-Well Plate (PCR-96-FS-C)\nSlot 3: Opentrons 10\u00b5L Tips", "internal": "4b76c0", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4c8861/README.json b/protoBuilds/4c8861/README.json index 2f0357175..29a0d41e6 100644 --- a/protoBuilds/4c8861/README.json +++ b/protoBuilds/4c8861/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol normalizes up to (3) 96 well plates with diluent from 3 source plates to 3 destination plates. Destination plates exactly mirror source plates. The protocol begins by transferring diluent to all relevant wells in all 3 plates (up to 96 for each plate), and then continues to do a 1-1 well to well transfer between the source and destination plates. A csv is parsed to determine the transfer volume for each well of each plate.\nSince the samples are temperature sensitive, the source plates are only loaded onto the deck one at a time, with the protocol pausing after all the diluent is added, and after each source plate is transferred. There is no mixing step in this protocol.\nExplanation of complex parameters below:\n* CSV Sample: Upload the csv sample with the following header line:\nPlate number | Well | Concentration (ng/ul) | Diluent Volume (ul) | Sample volume (ul) | Total volume (ul) | Desired concentration(ng/ul)\n* Reset Tipracks: Select yes to pick up the tip from A1 on the 200ul tip rack. Select no to pick up tip on the tip rack from where the previous run left off.\n* Include pauess: Select yes to include pause steps after buffer is added and in between source plates that are completed. Select no otherwise. \n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n* P300 Single-Channel Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n", + "description": "This protocol normalizes up to (3) 96 well plates with diluent from 3 source plates to 3 destination plates. Destination plates exactly mirror source plates. The protocol begins by transferring diluent to all relevant wells in all 3 plates (up to 96 for each plate), and then continues to do a 1-1 well to well transfer between the source and destination plates. A csv is parsed to determine the transfer volume for each well of each plate.\nSince the samples are temperature sensitive, the source plates are only loaded onto the deck one at a time, with the protocol pausing after all the diluent is added, and after each source plate is transferred. There is no mixing step in this protocol.\nExplanation of complex parameters below:\n CSV Sample: Upload the csv sample with the following header line:\nPlate number | Well | Concentration (ng/ul) | Diluent Volume (ul) | Sample volume (ul) | Total volume (ul) | Desired concentration(ng/ul)\n Reset Tipracks: Select yes to pick up the tip from A1 on the 200ul tip rack. Select no to pick up tip on the tip rack from where the previous run left off.\n Include pauess: Select yes to include pause steps after buffer is added and in between source plates that are completed. Select no otherwise. \n P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n* P300 Single-Channel Mount: Specify which mount (left or right) to host the P300 single-channel pipette.\n", "internal": "4c8861", "labware": "\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nOpentrons 4-in-1 Tuberack\nOpentrons 20ul Tips\nOpentrons 200ul Tips\n", "markdown": { diff --git a/protoBuilds/4d9b8b/README.json b/protoBuilds/4d9b8b/README.json index 4695090d1..096a0dddd 100644 --- a/protoBuilds/4d9b8b/README.json +++ b/protoBuilds/4d9b8b/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol drop casts a mixed solution of polymer to a silicon wafer. The protocol can be broken down into the following parts:\n\nMix 3 user-specified volumes (via CSV) of polymer in a mix plate.\nMix solutions, drop cast 1-1 transfer from mix plate onto silicon wafer.\n\nThe protocol begins by mixing 3 solutions of polymer (volumes of each respective solution specified by the user via a CSV file) in a 96 well plate, up to the number of samples specified. After a mix step, solutions are transferred 1-to-1 from the 96 well plate to the silicon wafer (A1 to A1, B1 to B1, etc.). The silicon wafer is treated as a 24, 48, or 96 well grid for this step, although in reality the surface is uniform.\nThe option to have various grid sizes is to vary spacing between drops. Depending on the solution volume, viscosity, dispense flow rate, and dispense height above the wafer, an appropriate grid can be chosen. \nExplanation of complex parameters below:\n* Number of Samples: Specify how many samples will be transferred onto the silicon wafer (number of wells).\n* CSV: Upload a CSV which specifies transfer volumes of the three solutions to be mixed and added to the silicon wafer.\nThe CSV should be formatted like so:\nWell | Transfer Volume Solution 1 (ul) | Transfer Volume Solution 2 (ul) | Transfer Volume Solution 3 (ul) | Transfer Volume to Silicon Plate (ul)\nExample Row: A1, 5, 10, 3, 18\nThe first row should contain headers (like above). All following rows should just include necessary information. \nSamples will be referenced in this protocol, as well as referenced in the CSV in order by column (e.g. A1, B1, C1, etc.) up to the number of samples for the run. The first Well column in the CSV should thus be ordered, A1, B1, C1, etc. \n* Dispense Height Above Wafer: Specify the height above the wafer to dispense mixed solution. Caution: a value of 0 returns the top of the wafer, with a value of 1 returning 1mm above the top of the wafer, for example. Negative numbers can also be passed (distance from top of the wafer) - use discretion to avoid tip crashing.\n* Dispense Flow Rate: Specify the dispense flow rate of solution onto the silicon wafer.\n* Mix Repetitions: Specify the number of times each well will be mixed in the mix well plate before being transferred onto the wafer.\n* Mix Volume: Specify the volume at which each well be mixed.\n* Initial Volume in Solution: Specify the initial volumes in all 3 tubes. This parameter is used for liquid tracking and ensuring the pipette is not submerged in solution.\n* Delay after dispense before returning tip: Specify the amount of time (in seconds) before the tip is returned to the tip rack after dispense. Following the dispense, there will be a delay, then blow out and touch tip. \n* P20 Single Mount: Specify which mount the P20 is on (left or right).\n", + "description": "This protocol drop casts a mixed solution of polymer to a silicon wafer. The protocol can be broken down into the following parts:\n\nMix 3 user-specified volumes (via CSV) of polymer in a mix plate.\nMix solutions, drop cast 1-1 transfer from mix plate onto silicon wafer.\n\nThe protocol begins by mixing 3 solutions of polymer (volumes of each respective solution specified by the user via a CSV file) in a 96 well plate, up to the number of samples specified. After a mix step, solutions are transferred 1-to-1 from the 96 well plate to the silicon wafer (A1 to A1, B1 to B1, etc.). The silicon wafer is treated as a 24, 48, or 96 well grid for this step, although in reality the surface is uniform.\nThe option to have various grid sizes is to vary spacing between drops. Depending on the solution volume, viscosity, dispense flow rate, and dispense height above the wafer, an appropriate grid can be chosen. \nExplanation of complex parameters below:\n Number of Samples: Specify how many samples will be transferred onto the silicon wafer (number of wells).\n CSV: Upload a CSV which specifies transfer volumes of the three solutions to be mixed and added to the silicon wafer.\nThe CSV should be formatted like so:\nWell | Transfer Volume Solution 1 (ul) | Transfer Volume Solution 2 (ul) | Transfer Volume Solution 3 (ul) | Transfer Volume to Silicon Plate (ul)\nExample Row: A1, 5, 10, 3, 18\nThe first row should contain headers (like above). All following rows should just include necessary information. \nSamples will be referenced in this protocol, as well as referenced in the CSV in order by column (e.g. A1, B1, C1, etc.) up to the number of samples for the run. The first Well column in the CSV should thus be ordered, A1, B1, C1, etc. \n Dispense Height Above Wafer: Specify the height above the wafer to dispense mixed solution. Caution: a value of 0 returns the top of the wafer, with a value of 1 returning 1mm above the top of the wafer, for example. Negative numbers can also be passed (distance from top of the wafer) - use discretion to avoid tip crashing.\n Dispense Flow Rate: Specify the dispense flow rate of solution onto the silicon wafer.\n Mix Repetitions: Specify the number of times each well will be mixed in the mix well plate before being transferred onto the wafer.\n Mix Volume: Specify the volume at which each well be mixed.\n Initial Volume in Solution: Specify the initial volumes in all 3 tubes. This parameter is used for liquid tracking and ensuring the pipette is not submerged in solution.\n Delay after dispense before returning tip: Specify the amount of time (in seconds) before the tip is returned to the tip rack after dispense. Following the dispense, there will be a delay, then blow out and touch tip. \n* P20 Single Mount: Specify which mount the P20 is on (left or right).\n", "internal": "4d9b8b", "labware": "\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nCostar 96 Well Plate\nSilicon Wafer with Opentrons Labware Adapter\nCustom 8-tube 20ml tube rack\n", "markdown": { diff --git a/protoBuilds/4ee4d6-part2/README.json b/protoBuilds/4ee4d6-part2/README.json index a3482b6ba..ce9056807 100644 --- a/protoBuilds/4ee4d6-part2/README.json +++ b/protoBuilds/4ee4d6-part2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module (Deck Slot 9)\nOpentrons Magnetic Module (Deck Slot 6)\nOpentrons p300 tips (Deck Slot 5)\nOpentrons p20 tips (Deck Slot 4)\nOpentrons Thermocycler Module (Deck Slots 7,8,10,11)\nreagents block (opentrons_24_aluminumblock_nest_2ml_snapcap) (Deck Slot 3)\nreagents reservoir (nest_12_reservoir_15ml) (Deck Slot 2)\n", - "description": "Part 2 of 2: Clean Up and Pool Libraries, Hybridize and Capture Probes, Amplify Enriched Library, Clean Up Enriched Library\nLinks:\n* Part 1: Tagmentation, Clean Up, Amplify Tagmented DNA\n* Part 2: Clean Up and Pool Libraries, Hybridize and Capture Probes, Amplify Enriched Library, Clean Up Enriched Library\n* Protocol\nWith this protocol, your robot can perform the Illumina DNA Prep with Enrichment protocol described by the Illumina DNA Prep with Enrichment Reference Guide.\nThis is part 2 of the protocol, which includes the steps (1) Clean Up and Pool Libraries (2) Hybridize and Capture Probes (3) Amplify Enriched Library and (4) Clean Up Enriched Library.\nThe first clean up uses a double-sided bead purification for consistently narrow fragment size distribution. Up to 12 libraries with unique indexes are combined into one pool. Streptavidin magnetic beads are used to capture probes hybridized to target sequences. The enriched library is then amplified by PCR.", + "description": "Part 2 of 2: Clean Up and Pool Libraries, Hybridize and Capture Probes, Amplify Enriched Library, Clean Up Enriched Library\nLinks:\n Part 1: Tagmentation, Clean Up, Amplify Tagmented DNA\n Part 2: Clean Up and Pool Libraries, Hybridize and Capture Probes, Amplify Enriched Library, Clean Up Enriched Library\n* Protocol\nWith this protocol, your robot can perform the Illumina DNA Prep with Enrichment protocol described by the Illumina DNA Prep with Enrichment Reference Guide.\nThis is part 2 of the protocol, which includes the steps (1) Clean Up and Pool Libraries (2) Hybridize and Capture Probes (3) Amplify Enriched Library and (4) Clean Up Enriched Library.\nThe first clean up uses a double-sided bead purification for consistently narrow fragment size distribution. Up to 12 libraries with unique indexes are combined into one pool. Streptavidin magnetic beads are used to capture probes hybridized to target sequences. The enriched library is then amplified by PCR.", "internal": "4ee4d6-part2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4ee4d6/README.json b/protoBuilds/4ee4d6/README.json index 30392ab2d..d3f75d7dd 100644 --- a/protoBuilds/4ee4d6/README.json +++ b/protoBuilds/4ee4d6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module (Deck Slot 9)\nOpentrons Magnetic Module (Deck Slot 6)\nOpentrons p300 tips (Deck Slot 5)\nOpentrons p20 tips (Deck Slot 4)\nOpentrons Thermocycler Module (Deck Slots 7,8,10,11)\ninitial samples (nest_96_wellplate_100ul_pcr_full_skirt) (Deck Slot 1)\nreagents block (opentrons_24_aluminumblock_nest_2ml_snapcap) (Deck Slot 3)\nreagents reservoir (nest_12_reservoir_15ml) (Deck Slot 2)\n", - "description": "Part 1 of 2: Tagmentation, Clean Up, Amplify Tagmented DNA\nLinks:\n* Part 1: Tagmentation, Clean Up, Amplify Tagmented DNA\n* Part 2: Clean Up and Pool Libraries, Hybridize and Capture Probes, Amplify Enriched Library, Clean Up Enriched Library\n* Protocol\nWith this protocol, your robot can perform the Illumina DNA Prep with Enrichment protocol described by the Illumina DNA Prep with Enrichment Reference Guide.\nThis is part 1 of the protocol, which includes the steps (1) Tagmentation (2) Clean Up and (3) Amplify Tagmented DNA.\nThe tagmentation uses a bead-based transposome complex to fragment a set number (if saturated with input DNA, the process is self-normalizing) of genomic DNA molecules and tag them with adapter sequences in one step. The amplification step increases the yield, adds indexes, and enables capability across all Illumina sequencing platforms.\nAfter the steps carried out in this protocol, you can safely stop work and return to it at a later point. If you are stopping, store at -25\u00b0C to -15\u00b0C for up to 30 days.", + "description": "Part 1 of 2: Tagmentation, Clean Up, Amplify Tagmented DNA\nLinks:\n Part 1: Tagmentation, Clean Up, Amplify Tagmented DNA\n Part 2: Clean Up and Pool Libraries, Hybridize and Capture Probes, Amplify Enriched Library, Clean Up Enriched Library\n* Protocol\nWith this protocol, your robot can perform the Illumina DNA Prep with Enrichment protocol described by the Illumina DNA Prep with Enrichment Reference Guide.\nThis is part 1 of the protocol, which includes the steps (1) Tagmentation (2) Clean Up and (3) Amplify Tagmented DNA.\nThe tagmentation uses a bead-based transposome complex to fragment a set number (if saturated with input DNA, the process is self-normalizing) of genomic DNA molecules and tag them with adapter sequences in one step. The amplification step increases the yield, adds indexes, and enables capability across all Illumina sequencing platforms.\nAfter the steps carried out in this protocol, you can safely stop work and return to it at a later point. If you are stopping, store at -25\u00b0C to -15\u00b0C for up to 30 days.", "internal": "4ee4d6", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/4f7a6f/README.json b/protoBuilds/4f7a6f/README.json index ed6f888f6..81fedec29 100644 --- a/protoBuilds/4f7a6f/README.json +++ b/protoBuilds/4f7a6f/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol performs an equilibrium dialysis assay on the OT-2 using HTD plates. The HTD plate is mounted directly on the temperature module to achieve cooling, as well as the buffer. Backup buffer reservoirs are available on the deck, as well as waste reservoirs. A csv is uploaded to the protocol to gain information such as transfer volume, incubation time, and buffer volume. The OT-2 will only be accessing the bottom half of the wells for the duration of the protocol, so as to operate below the partition line. For detailed protocol steps, please see below.\nExplanation of complex parameters below:\n* csv: Here, you should upload a .csv file formatted in the following way, being sure to include the header line (note sample number should always be in multiples of 8 e.g. 8, 16, 24, 32, etc.):\nN.\u00ba PROTEIN,VOLUME_EXCHANGE (ul) | VOLUME_RESERVOIR (ml) | TEMPERATURE_MODULE 1 (\u00baC) | TEMPERATURE_MODULE 2 (\u00baC) | TIME_PROTOCOL (min) | TIME_INCUBATE (min)\n96,300,195,4,4,840,30\n* Initial volume of buffer reservoir: Specify the volume inside each of the reservoirs in mL.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel pipette.\n", + "description": "This protocol performs an equilibrium dialysis assay on the OT-2 using HTD plates. The HTD plate is mounted directly on the temperature module to achieve cooling, as well as the buffer. Backup buffer reservoirs are available on the deck, as well as waste reservoirs. A csv is uploaded to the protocol to gain information such as transfer volume, incubation time, and buffer volume. The OT-2 will only be accessing the bottom half of the wells for the duration of the protocol, so as to operate below the partition line. For detailed protocol steps, please see below.\nExplanation of complex parameters below:\n csv: Here, you should upload a .csv file formatted in the following way, being sure to include the header line (note sample number should always be in multiples of 8 e.g. 8, 16, 24, 32, etc.):\nN.\u00ba PROTEIN,VOLUME_EXCHANGE (ul) | VOLUME_RESERVOIR (ml) | TEMPERATURE_MODULE 1 (\u00baC) | TEMPERATURE_MODULE 2 (\u00baC) | TIME_PROTOCOL (min) | TIME_INCUBATE (min)\n96,300,195,4,4,840,30\n Initial volume of buffer reservoir: Specify the volume inside each of the reservoirs in mL.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel pipette.\n", "internal": "4f7a64", "labware": "\nNEST 1-Well Reservoirs, 195 mL\n*Opentrons 300\u00b5L Tips\nHTD Dialysis Plate\n", "markdown": { diff --git a/protoBuilds/4fc750/README.json b/protoBuilds/4fc750/README.json index d7416dcdb..874bcf0e7 100644 --- a/protoBuilds/4fc750/README.json +++ b/protoBuilds/4fc750/README.json @@ -5,7 +5,7 @@ "Omega Mag-Bind\u00ae Blood & Tissue DNA 96 Kit" ] }, - "description": "This is a flexible protocol accommodating the framework given for the 250\u00b5l Blood Protocol in the Omega Mag-Bind\u00ae Blood & Tissue DNA 96 Kit,\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 1) to the elution PCR plate (slot 5). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nNEST 12 Well Reservoir 15 mL or USA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL or Agilent 1 Well Reservoir 290 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt or Bio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 96 Deepwell Plate 2mL or USA Scientific 96 Deep Well Plate 2.4 mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n", + "description": "This is a flexible protocol accommodating the framework given for the 250\u00b5l Blood Protocol in the Omega Mag-Bind\u00ae Blood & Tissue DNA 96 Kit,\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 1) to the elution PCR plate (slot 5). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nNEST 12 Well Reservoir 15 mL or USA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL or Agilent 1 Well Reservoir 290 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt or Bio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 96 Deepwell Plate 2mL or USA Scientific 96 Deep Well Plate 2.4 mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n", "internal": "4fc750", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/50c11b/README.json b/protoBuilds/50c11b/README.json index 2631dd29d..07a4c7ee3 100644 --- a/protoBuilds/50c11b/README.json +++ b/protoBuilds/50c11b/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "The deck should be setup as follows:\n\n\nTipracks: These will be accessed in the numbered order (starting with slot 8 and ending with slot 7)\nSample Plates: These can be loaded as needed and with as many samples as available, with the locations of plates being static. In the image above, Plates 1 and 2 are loaded completely while Plates 3 and 4 only have 16 samples.\nDestination Plate: This is the 384-well plate and should be pre-filled with the corresponding mastermix needed for the protocol.", - "description": "This protocol automates two different PCR setup protocols, transferring up to 96 samples from up to 4 different source plates to a single 384-well plate.\nUsing the P20 8-Channel Pipette (GEN2), samples are transferred from KingFisher 96-Deepwell plates to an Applied Biosystems MicroAmp Optical 384-Well Reaction Plate (pre-filled with mastermix), mixing the samples slightly before transfer and again after transfer.\nTo optimize waste bin storage and reduce the need for human interference, tips used after the first plate of transfers are replaced in the empty tiprack slots from the earlier transfers (ex. tips used for Plate 2 transfers are replaced in the tiprack used for Plate 1 transfers).\nExplanation of complex parameters below:\n* Protocol Type: If set to Covid, 5.3\u00b5l of sample will be transferred to the destination plate and 12\u00b5L will be mixed within the well. If set to UTI & More, 2\u00b5l of sample will be transferred to the destination plate and 4\u00b5L will be mixed within the well.\n* Plate 1 Number of Samples: Specify the number of samples in Plate 1 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* Plate 2 Number of Samples: Specify the number of samples in Plate 2 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* Plate 3 Number of Samples: Specify the number of samples in Plate 3 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* Plate 4 Number of Samples: Specify the number of samples in Plate 4 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n* P20-Multi Mount: Select which mount the P20-Multi Pipette is attached to.\n", + "description": "This protocol automates two different PCR setup protocols, transferring up to 96 samples from up to 4 different source plates to a single 384-well plate.\nUsing the P20 8-Channel Pipette (GEN2), samples are transferred from KingFisher 96-Deepwell plates to an Applied Biosystems MicroAmp Optical 384-Well Reaction Plate (pre-filled with mastermix), mixing the samples slightly before transfer and again after transfer.\nTo optimize waste bin storage and reduce the need for human interference, tips used after the first plate of transfers are replaced in the empty tiprack slots from the earlier transfers (ex. tips used for Plate 2 transfers are replaced in the tiprack used for Plate 1 transfers).\nExplanation of complex parameters below:\n Protocol Type: If set to Covid, 5.3\u00b5l of sample will be transferred to the destination plate and 12\u00b5L will be mixed within the well. If set to UTI & More, 2\u00b5l of sample will be transferred to the destination plate and 4\u00b5L will be mixed within the well.\n Plate 1 Number of Samples: Specify the number of samples in Plate 1 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n Plate 2 Number of Samples: Specify the number of samples in Plate 2 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n Plate 3 Number of Samples: Specify the number of samples in Plate 3 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n Plate 4 Number of Samples: Specify the number of samples in Plate 4 (up to 96). The plate can be skipped by setting this value to 0 (zero).\n P20-Multi Mount: Select which mount the P20-Multi Pipette is attached to.\n", "internal": "50c11b", "labware": "\nOpentrons 20\u00b5L Filter Tips\nKingFisher 96 Deepwell Plate (containing samples)\nApplied Biosystems MicroAmp Optical 384-Well Reaction Plate\n", "markdown": { diff --git a/protoBuilds/516336-part-2/README.json b/protoBuilds/516336-part-2/README.json index ccf4b5810..658c9bff5 100644 --- a/protoBuilds/516336-part-2/README.json +++ b/protoBuilds/516336-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates the Adapter Ligation and Clean-Up portion for preparing sequencing libraries in the Oxford Nanopore Ligation Sequencing Kit. There is a first part of this protocol for the DNA Repair and End-Prep.\nExplanation of parameters below:\n* Number of Samples: Specify the number of samples in multiples of 8 (Max: 96).\n* P300 Multichannel GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n* P300 Single GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n* Magnetic Module Engage Height from Well Bottom (mm): Specify the height of the magnets from the bottom of the well.\n", + "description": "This protocol automates the Adapter Ligation and Clean-Up portion for preparing sequencing libraries in the Oxford Nanopore Ligation Sequencing Kit. There is a first part of this protocol for the DNA Repair and End-Prep.\nExplanation of parameters below:\n Number of Samples: Specify the number of samples in multiples of 8 (Max: 96).\n P300 Multichannel GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n P300 Single GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n Magnetic Module Engage Height from Well Bottom (mm): Specify the height of the magnets from the bottom of the well.\n", "internal": "516336-part-2", "labware": "\nThermoFisher 96 Well 0.8mL Polypropylene Deepwell Storage Plate\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 300uL Tips\n", "markdown": { diff --git a/protoBuilds/516336/README.json b/protoBuilds/516336/README.json index 19b1759fa..763b20097 100644 --- a/protoBuilds/516336/README.json +++ b/protoBuilds/516336/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates the DNA Repair and End Prep portion for preparing sequencing libraries in the Oxford Nanopore Ligation Sequencing Kit. The second part of this protocol can be found here: Adapter Ligation and Clean-Up\n\nNote: The protocol was updated on September 22nd, 2022\n\nExplanation of parameters below:\n* Number of Samples: Specify the number of samples in multiples of 8 (Max: 96).\n* P300 Multichannel GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n* P300 Single GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n* Magnetic Module Generation: Specify whether using Gen 1 or Gen 2 magnetic module.\n* Magnetic Module Engage Height from Well Bottom (mm): Specify the height of the magnets from the bottom of the well.\n", + "description": "This protocol automates the DNA Repair and End Prep portion for preparing sequencing libraries in the Oxford Nanopore Ligation Sequencing Kit. The second part of this protocol can be found here: Adapter Ligation and Clean-Up\n\nNote: The protocol was updated on September 22nd, 2022\n\nExplanation of parameters below:\n Number of Samples: Specify the number of samples in multiples of 8 (Max: 96).\n P300 Multichannel GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n P300 Single GEN2 Mount Position: Specify the mount position of the P300 Multichannel.\n Magnetic Module Generation: Specify whether using Gen 1 or Gen 2 magnetic module.\n* Magnetic Module Engage Height from Well Bottom (mm): Specify the height of the magnets from the bottom of the well.\n", "internal": "516336", "labware": "\nThermoFisher 96 Well 0.8mL Polypropylene Deepwell Storage Plate\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 300uL Tips\n", "markdown": { diff --git a/protoBuilds/5191b6/README.json b/protoBuilds/5191b6/README.json index 5db832adb..e96d2e481 100644 --- a/protoBuilds/5191b6/README.json +++ b/protoBuilds/5191b6/README.json @@ -5,7 +5,7 @@ "Cherrypicking" ] }, - "description": "This protocol performs a custom cherrypicked high-throughput synthesis. It requires a CSV input for the mapping of the wells and vials on the tube racks. It also requires a CSV for high-throughput synthesis which contains the dispending volumes from each reservoir.\n\n\n\nP1000 single-channel GEN2 electronic pipette\nP300 single-channel GEN2 electronic pipette\nOpentrons Tube Racks\n\n\n\n\nVial Map CSV Example\nHigh-Throughput CSV Example\n\nDeck Setup\n* P1000 Tips (Slot 1)\n* P300 Tips (Slot 2)\n* Reagent Reservoirs (Use High-Throughput CSV)\n* Opentrons Tube Racks (Use Vial Map CSV)\nExample of the Vial Map CSV Download Example:\nWell Number,Labware,Slot,Well Position\n1,opentrons_24_tuberack_nest_2ml_screwcap,4,A1\n2,opentrons_24_tuberack_nest_2ml_screwcap,4,A2\n3,opentrons_24_tuberack_nest_2ml_screwcap,4,A3\n...\n96,opentrons_24_tuberack_nest_2ml_screwcap,7,D6\nThe Vial Map CSV can be used to place custom labware and different tube racks from the labware library. It also allows mapping of the well positions of each vial on a tube rack corresponding to the well number in the high-throughput synthesis protocol.\nExample of the High-Throughput Synthesis Protocol CSV Download Example\n*Note numbering starts from top left to top right,Reservoir 1,Reservoir 2,Reservoir 3,Reservoir 4,Reservoir 5,Reservoir 6,Reservoir 7,Reservoir 8,Reservoir 9,Reservoir 10,Reservoir 11,Reservoir 12,Reservoir 13,Reservoir 14,Reservoir 15,\nLabware,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,\nSlot,3,3,3,3,3,3,8,8,8,8,8,9,9,9,9,\nWell Position,A1,B1,C1,A2,B2,C2,A3,B3,C3,A4,B4,C4,A5,B5,C5,\nWell Number,Metal Salt Stock Soln 1 (1 M) (uL),Metal Salt Stock Soln 2 (1 M) (uL),Metal Salt Stock Soln 3 (1 M) (uL),Metal Salt Stock Soln 4 (1 M) (uL),Organic Linker Stock Soln 1 (1 M) (uL),Organic Linker Stock Soln 2 (1 M) (uL),Organic Linker Stock Soln 3 (1 M) (uL),Organic Linker Stock Soln 4 (1M) (uL),Extra Solvent 1 (uL),Extra Solvent 2 (uL),Extra Solvent 3 (uL),Extra Solvent 4 (uL),,,,Total Volume (uL)\n1,270,270,270,150,150,150,150,150,64,64,150,150,270,150,270,1088\n2,27,270,270,150,150,150,150,150,48,48,150,150,27,150,27,813\n3,34,270,270,150,150,150,150,150,48,48,150,150,34,150,34,821", + "description": "This protocol performs a custom cherrypicked high-throughput synthesis. It requires a CSV input for the mapping of the wells and vials on the tube racks. It also requires a CSV for high-throughput synthesis which contains the dispending volumes from each reservoir.\n\n\n\nP1000 single-channel GEN2 electronic pipette\nP300 single-channel GEN2 electronic pipette\nOpentrons Tube Racks\n\n\n\n\nVial Map CSV Example\nHigh-Throughput CSV Example\n\nDeck Setup\n P1000 Tips (Slot 1)\n P300 Tips (Slot 2)\n Reagent Reservoirs (Use High-Throughput CSV)\n Opentrons Tube Racks (Use Vial Map CSV)\nExample of the Vial Map CSV Download Example:\nWell Number,Labware,Slot,Well Position\n1,opentrons_24_tuberack_nest_2ml_screwcap,4,A1\n2,opentrons_24_tuberack_nest_2ml_screwcap,4,A2\n3,opentrons_24_tuberack_nest_2ml_screwcap,4,A3\n...\n96,opentrons_24_tuberack_nest_2ml_screwcap,7,D6\nThe Vial Map CSV can be used to place custom labware and different tube racks from the labware library. It also allows mapping of the well positions of each vial on a tube rack corresponding to the well number in the high-throughput synthesis protocol.\nExample of the High-Throughput Synthesis Protocol CSV Download Example\n*Note numbering starts from top left to top right,Reservoir 1,Reservoir 2,Reservoir 3,Reservoir 4,Reservoir 5,Reservoir 6,Reservoir 7,Reservoir 8,Reservoir 9,Reservoir 10,Reservoir 11,Reservoir 12,Reservoir 13,Reservoir 14,Reservoir 15,\nLabware,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,rssrack_15_tuberack_2500ul,\nSlot,3,3,3,3,3,3,8,8,8,8,8,9,9,9,9,\nWell Position,A1,B1,C1,A2,B2,C2,A3,B3,C3,A4,B4,C4,A5,B5,C5,\nWell Number,Metal Salt Stock Soln 1 (1 M) (uL),Metal Salt Stock Soln 2 (1 M) (uL),Metal Salt Stock Soln 3 (1 M) (uL),Metal Salt Stock Soln 4 (1 M) (uL),Organic Linker Stock Soln 1 (1 M) (uL),Organic Linker Stock Soln 2 (1 M) (uL),Organic Linker Stock Soln 3 (1 M) (uL),Organic Linker Stock Soln 4 (1M) (uL),Extra Solvent 1 (uL),Extra Solvent 2 (uL),Extra Solvent 3 (uL),Extra Solvent 4 (uL),,,,Total Volume (uL)\n1,270,270,270,150,150,150,150,150,64,64,150,150,270,150,270,1088\n2,27,270,270,150,150,150,150,150,48,48,150,150,27,150,27,813\n3,34,270,270,150,150,150,150,150,48,48,150,150,34,150,34,821", "internal": "5191b6", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/51df08/README.json b/protoBuilds/51df08/README.json index 0c1e18143..360dc8c09 100644 --- a/protoBuilds/51df08/README.json +++ b/protoBuilds/51df08/README.json @@ -5,7 +5,7 @@ "Assay" ] }, - "description": "This protocol performs a mass spec sample prep on up to 10 samples with up to 5 antibodies on up to 2 custom 72-sample slide mounts (the top row of 9 wells are left blank). Samples and antibodies should be loaded in their respective tuberacks down the columns and then across the rows. Samples and antibodies are filled in the slides down the first column of each slide, then up the second, and finally down the third column. For more detailed sample and reagent setup, please see below.\n\n\n\ncustom 3-grid 3x8 slide mount\nOpentrons 4x6 tuberack insert with 1.5ml Eppendorf snapcap tubes\nOpentrons 2x3 tuberack insert with 50ml Falcon tubes\nOpentrons 20ul pipette tips\nOpentrons 300ul pipette tips\nOpentrons P20- and P300-single GEN2 electronic pipettes\n\n\n\n2x3 50ml tuberack (slot 1)\n* detergent wash buffer: tube A1\n* BSA blocking buffer: tube B1\n* PBS: tubes A2-B2\n* water: tubes A3-B3", + "description": "This protocol performs a mass spec sample prep on up to 10 samples with up to 5 antibodies on up to 2 custom 72-sample slide mounts (the top row of 9 wells are left blank). Samples and antibodies should be loaded in their respective tuberacks down the columns and then across the rows. Samples and antibodies are filled in the slides down the first column of each slide, then up the second, and finally down the third column. For more detailed sample and reagent setup, please see below.\n\n\n\ncustom 3-grid 3x8 slide mount\nOpentrons 4x6 tuberack insert with 1.5ml Eppendorf snapcap tubes\nOpentrons 2x3 tuberack insert with 50ml Falcon tubes\nOpentrons 20ul pipette tips\nOpentrons 300ul pipette tips\nOpentrons P20- and P300-single GEN2 electronic pipettes\n\n\n\n2x3 50ml tuberack (slot 1)\n detergent wash buffer: tube A1\n BSA blocking buffer: tube B1\n PBS: tubes A2-B2\n water: tubes A3-B3", "internal": "51df08", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/528c16/README.json b/protoBuilds/528c16/README.json index 6ec925231..0168eec79 100644 --- a/protoBuilds/528c16/README.json +++ b/protoBuilds/528c16/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps 1.5mL and 2mL tubes from stock solutions including but not limited to acetonitrile, water, and methanol. Sources and destinations are determined via a csv uploaded by the user, as well as transfer volumes.\nExplanation of complex parameters below:\n* csv file: The csv file should be formatted like so. Note - for no mix steps, input \"0\" for the mix repetition. Also specify whether to mix at the source, or destination tube for that row:\n\n* Note: for aspiration height percent (column J), a value of 10 means that we will be aspirating from 10% of the tube depth, 50 will be 50% of the tube depth, etc.\n* P20/P1000 Mount: Specify which mount (left or right) for each single channel pipette.\n", + "description": "This protocol preps 1.5mL and 2mL tubes from stock solutions including but not limited to acetonitrile, water, and methanol. Sources and destinations are determined via a csv uploaded by the user, as well as transfer volumes.\nExplanation of complex parameters below:\n* csv file: The csv file should be formatted like so. Note - for no mix steps, input \"0\" for the mix repetition. Also specify whether to mix at the source, or destination tube for that row:\n\n Note: for aspiration height percent (column J), a value of 10 means that we will be aspirating from 10% of the tube depth, 50 will be 50% of the tube depth, etc.\n P20/P1000 Mount: Specify which mount (left or right) for each single channel pipette.\n", "internal": "528c16", "labware": "\nOpentrons 4-in-1 tube rack with 50mL & 15mL Falcon tubes\nOpentrons 4-in-1 tube rack with 1.5mL Eppendorf snap cap tubes\nOpentrons 1000ul tips\nOpentrons 20ul tips\n", "markdown": { diff --git a/protoBuilds/53e6bc_mastermix_creation/README.json b/protoBuilds/53e6bc_mastermix_creation/README.json index 5bdcd9eec..f28c0c631 100644 --- a/protoBuilds/53e6bc_mastermix_creation/README.json +++ b/protoBuilds/53e6bc_mastermix_creation/README.json @@ -5,7 +5,7 @@ "Assay" ] }, - "description": "This protocol performs custom mastermix creation from antibodies. The volumes of each antibody per sample to be transferred from a custom deepwell plate to the mastermix tube are specfied in a .csv input file, formatted as follows:\nVolume per antibody(in ul),Antibody,Well\n2.2,CD3 BUV395,A1\n1.1,CD45 BUV496,A3\n1.1,CD15 BUV563,A5\n1.1,CD45RA BUV615,A7\n2.2,CD14 BUV661,A9\n0.55,CD8 BUV737,A11\n2.2,CD11c BUV805,B2\n1.1,CD25 BV421,B4\n0.55,CD4 BV480,B6\n2.2,CD16 BV605,B8\n2.2,CD123 BV650,B10\n2.2,CD127 BV711,B12\n2.2,IgD BV750,C1\n2.2,CD304 BV786,C3\n2.2,CD141 BB515,C5\nNote that the headers line should be included, and empty lines are ignored.\nLinks:\n* Flow Cytometry Staining\n\n\n\nVWR 96-deepwell plate 2.2ml #10755-250\nVWR conical self-standing tubes 5ml #89497-740 (or equivalent) seated in Opentrons 4-in-1 tuberack with 3x5 insert\nVWR screwcap microcentrifuge tubes 1.5ml # (or equivalent) seated in Opentrons 4-in-1 tuberack with 4x6 insert\nOpentrons P300 GEN1 single-channel pipette\nOpentrons P10 GEN1 single-channel pipette\nOpentrons 300ul tiprack\nOpentrons 10ul tiprack\n\n\n\n3x5 tuberack for 5ml screwcap tubes (slot 2)\n* tube A1: mastermix (loaded empty)\n* tube B1: PBS\n4x6 tuberack for 1.5ml screwcap tubes (slot 4)\n* tube A1: Brilliant Stain Buffer", + "description": "This protocol performs custom mastermix creation from antibodies. The volumes of each antibody per sample to be transferred from a custom deepwell plate to the mastermix tube are specfied in a .csv input file, formatted as follows:\nVolume per antibody(in ul),Antibody,Well\n2.2,CD3 BUV395,A1\n1.1,CD45 BUV496,A3\n1.1,CD15 BUV563,A5\n1.1,CD45RA BUV615,A7\n2.2,CD14 BUV661,A9\n0.55,CD8 BUV737,A11\n2.2,CD11c BUV805,B2\n1.1,CD25 BV421,B4\n0.55,CD4 BV480,B6\n2.2,CD16 BV605,B8\n2.2,CD123 BV650,B10\n2.2,CD127 BV711,B12\n2.2,IgD BV750,C1\n2.2,CD304 BV786,C3\n2.2,CD141 BB515,C5\nNote that the headers line should be included, and empty lines are ignored.\nLinks:\n* Flow Cytometry Staining\n\n\n\nVWR 96-deepwell plate 2.2ml #10755-250\nVWR conical self-standing tubes 5ml #89497-740 (or equivalent) seated in Opentrons 4-in-1 tuberack with 3x5 insert\nVWR screwcap microcentrifuge tubes 1.5ml # (or equivalent) seated in Opentrons 4-in-1 tuberack with 4x6 insert\nOpentrons P300 GEN1 single-channel pipette\nOpentrons P10 GEN1 single-channel pipette\nOpentrons 300ul tiprack\nOpentrons 10ul tiprack\n\n\n\n3x5 tuberack for 5ml screwcap tubes (slot 2)\n tube A1: mastermix (loaded empty)\n tube B1: PBS\n4x6 tuberack for 1.5ml screwcap tubes (slot 4)\n* tube A1: Brilliant Stain Buffer", "internal": "53e6bc", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/53fec2/README.json b/protoBuilds/53fec2/README.json index 9f28da265..d6592ea9b 100644 --- a/protoBuilds/53fec2/README.json +++ b/protoBuilds/53fec2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This is a flexible protocol accommodating Beckman Coulter AMPure XP PCR Cleanup and Size Selection. It consists of the following major sections:\n* binding beads pre-addition\n* sample pooling and mixing with binding beads\n* 2x ethanol wash\n* final elution in H2O\nSamples to be pooled should be loaded in 2 PCR plates on the deck. For reagent layout used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 7) to the elution PCR plate (slot 8). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", + "description": "This is a flexible protocol accommodating Beckman Coulter AMPure XP PCR Cleanup and Size Selection. It consists of the following major sections:\n binding beads pre-addition\n sample pooling and mixing with binding beads\n 2x ethanol wash\n final elution in H2O\nSamples to be pooled should be loaded in 2 PCR plates on the deck. For reagent layout used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 7) to the elution PCR plate (slot 8). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", "internal": "53fec2", "labware": "\nEppendorf 96-deepwell plate 500\u00b5l\nEppendorf 96-well PCR plate 200\u00b5l, skirted\nEppendorf 1-channel automation reservoirs 30ml/100ml\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/5689f5/README.json b/protoBuilds/5689f5/README.json index c3f68d48f..a9351f1cb 100644 --- a/protoBuilds/5689f5/README.json +++ b/protoBuilds/5689f5/README.json @@ -5,7 +5,7 @@ "Clean Up" ] }, - "deck-setup": "\n* green on magnetic plate (slot 4): starting samples\n* blue on reagent plate (slot 2, column 1): DNA binding buffer\n* pink on reagent plate (slot 2, column 2): Ampure beads\n* orange on reagent plate (slot 2, column 3): elution buffer\n* purple on reagent reservoir (slot 5, column 1): 80% ethanol\n* dark blue on reagent reservoir (slot 5, column 12): waste (loaded empty)", + "deck-setup": "\n green on magnetic plate (slot 4): starting samples\n blue on reagent plate (slot 2, column 1): DNA binding buffer\n pink on reagent plate (slot 2, column 2): Ampure beads\n orange on reagent plate (slot 2, column 3): elution buffer\n purple on reagent reservoir (slot 5, column 1): 80% ethanol\n dark blue on reagent reservoir (slot 5, column 12): waste (loaded empty)", "description": "This protocol performs an NGS clean up protocol for up to 96 samples. The user is prompted to manually centrifuge the plate and replace on the magnetic module after 2x ethanol washes.", "internal": "5689f5", "labware": "\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt #402501\nNEST 12 Well Reservoir 15 mL #360102\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", diff --git a/protoBuilds/56a6a1/README.json b/protoBuilds/56a6a1/README.json index 3b3d3c986..02bb2e62a 100644 --- a/protoBuilds/56a6a1/README.json +++ b/protoBuilds/56a6a1/README.json @@ -5,7 +5,7 @@ "Assay" ] }, - "description": "This protocol performs a protein array on ONCYTE SuperNOVA slides mounted on an Inheco Teleshake 1536 using a P300 multi-channel pipette. For reagent setup in the 12-channel reservoir, see 'Additional Notes' below. Note that the user is prompted three times to engage and disengage the shaker (mounted on the deck). The Teleshake with slides will occupy slots 1, 2, 4, and 5, and will be calibrated from slot 4.\n\n\n\nGrace ONCYTE SuperNOVA 16-well slides #705116\nCustom 4-slide adapter for Inheco Teleshake 1536 (each slide with 8x2 square wells)\nBio-Rad Hard Shell 96-Well PCR plate 200ul #hsp9601 (if automatically adding samples)\nAgilent 1-Well Reservoir 290mL #201252-100\nUSA Scientific 12-Well Reservoir 22mL #1061-8150\nOpentrons P300 multi-channel electronic pipette\nOpentrons 300ul pipette tips\nInheco Teleshake 1536\n\n\n\n12-channel reservoir\n* Super G plus blocking buffer: channel 1\n* Secondary antibody: channel 2\n* PBST: channels 3-6\n* Super G: channel 7", + "description": "This protocol performs a protein array on ONCYTE SuperNOVA slides mounted on an Inheco Teleshake 1536 using a P300 multi-channel pipette. For reagent setup in the 12-channel reservoir, see 'Additional Notes' below. Note that the user is prompted three times to engage and disengage the shaker (mounted on the deck). The Teleshake with slides will occupy slots 1, 2, 4, and 5, and will be calibrated from slot 4.\n\n\n\nGrace ONCYTE SuperNOVA 16-well slides #705116\nCustom 4-slide adapter for Inheco Teleshake 1536 (each slide with 8x2 square wells)\nBio-Rad Hard Shell 96-Well PCR plate 200ul #hsp9601 (if automatically adding samples)\nAgilent 1-Well Reservoir 290mL #201252-100\nUSA Scientific 12-Well Reservoir 22mL #1061-8150\nOpentrons P300 multi-channel electronic pipette\nOpentrons 300ul pipette tips\nInheco Teleshake 1536\n\n\n\n12-channel reservoir\n Super G plus blocking buffer: channel 1\n Secondary antibody: channel 2\n PBST: channels 3-6\n Super G: channel 7", "internal": "56a6a1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/56b4ec/README.json b/protoBuilds/56b4ec/README.json index acce3f464..bbd51de9c 100644 --- a/protoBuilds/56b4ec/README.json +++ b/protoBuilds/56b4ec/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol performs all of the steps as outlined in the MethodA_map_labware_protocol file. This protocol requires the use of custom labware (Charles River Tube Rack) and custom tips (200\u00b5L, extended length).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P50 Single Pipette\nOpentrons P1000 Single Pipette\nOpentrons 1000\u00b5L Filter Tips\nOpentrons 4-in-1 Tube Rack\nCorning 96-Well Plate, 360\u00b5L\nCustom 200\u00b5L Tips\nCustom Tube Rack for 10mL Charles River Tubes\nFalcon 50mL Conical Tube\nEppendorf 2mL Tubes\n\n\n\nSlot 1: Custom 200\u00b5L Tips\nSlot 2: Opentrons 1000\u00b5L Filter Tips\nSlot 3: Corning 96-Well Plate, 360\u00b5L\nSlot 4: Empty\nSlot 5: Empty\nSlot 6: Empty\nSlot 7: Opentrons 6 Tube Rack with 50mL Tube (Rack for water)\n* A1: Water, 30mL\nSlot 8: Custom Charles River Tube Rack (Rack for sample 1 dilution)\n* A1: Sample 1, 4mL\n* A2: Charles River Tube, empty\n* A3: Charles River Tube, empty\n* A4: Charles River Tube, empty\n* B1: Charles River Tube, empty\n* B2: Charles River Tube, empty\n* B3: Charles River Tube, empty\n* B4: Charles River Tube, empty\nSlot 9: Empty\nSlot 10: Opentrons 24 Tube Rack with 2mL Tubes (Rack for RSE & NEP)\n* A1: RSE, 1mL\n* A2: HKSA, 500\u00b5L\nSlot 11: Custom Charles River Tube Rack (Rack for RSE & HKSA dilution)\n* A1: Charles River Tube, empty\n* A2: Charles River Tube, empty\n* A3: Charles River Tube, empty\n* A4: Charles River Tube, empty\n* A5: Charles River Tube, empty\n* B1: Charles River Tube, empty\n* B2: Charles River Tube, empty\n* B3: Charles River Tube, empty\n* C1: Charles River Tube, empty\n* C2: Charles River Tube, empty", + "description": "This protocol performs all of the steps as outlined in the MethodA_map_labware_protocol file. This protocol requires the use of custom labware (Charles River Tube Rack) and custom tips (200\u00b5L, extended length).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P50 Single Pipette\nOpentrons P1000 Single Pipette\nOpentrons 1000\u00b5L Filter Tips\nOpentrons 4-in-1 Tube Rack\nCorning 96-Well Plate, 360\u00b5L\nCustom 200\u00b5L Tips\nCustom Tube Rack for 10mL Charles River Tubes\nFalcon 50mL Conical Tube\nEppendorf 2mL Tubes\n\n\n\nSlot 1: Custom 200\u00b5L Tips\nSlot 2: Opentrons 1000\u00b5L Filter Tips\nSlot 3: Corning 96-Well Plate, 360\u00b5L\nSlot 4: Empty\nSlot 5: Empty\nSlot 6: Empty\nSlot 7: Opentrons 6 Tube Rack with 50mL Tube (Rack for water)\n* A1: Water, 30mL\nSlot 8: Custom Charles River Tube Rack (Rack for sample 1 dilution)\n A1: Sample 1, 4mL\n A2: Charles River Tube, empty\n A3: Charles River Tube, empty\n A4: Charles River Tube, empty\n B1: Charles River Tube, empty\n B2: Charles River Tube, empty\n B3: Charles River Tube, empty\n B4: Charles River Tube, empty\nSlot 9: Empty\nSlot 10: Opentrons 24 Tube Rack with 2mL Tubes (Rack for RSE & NEP)\n A1: RSE, 1mL\n A2: HKSA, 500\u00b5L\nSlot 11: Custom Charles River Tube Rack (Rack for RSE & HKSA dilution)\n A1: Charles River Tube, empty\n A2: Charles River Tube, empty\n A3: Charles River Tube, empty\n A4: Charles River Tube, empty\n A5: Charles River Tube, empty\n B1: Charles River Tube, empty\n B2: Charles River Tube, empty\n B3: Charles River Tube, empty\n C1: Charles River Tube, empty\n C2: Charles River Tube, empty", "internal": "56b4ec", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/581011-pt2/README.json b/protoBuilds/581011-pt2/README.json index 39dde6d7b..b548e9d1b 100644 --- a/protoBuilds/581011-pt2/README.json +++ b/protoBuilds/581011-pt2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck layout - example 384 plate populated with target cells, random column chosen for effector cells. Note: only one column of effector cells should be loaded, but any column can be loaded. Effector cells should always be put in the 96 well plate from row A down (i.e. effector cell 1 should always be A1, A2, A3, A4,..., or A12).\n\n\n", - "description": "This protocol parses an uploaded .csv file (see below) and determines the number of tips to pick up with a multi-channel pipette. The pipette transfers the specified volume of effector cell to a 384 well-plate to the parsed wells by multi-dispensing as much as the pipette tip can accommodate before returning to the reservoir. The pipette keeps the same tip for the duration of the run.\nNote: Part 1 and Part 2 should receive the exact same .csv file.\nFind part one of the protocol (target cell loading) below:\nPart 1 - Target Cell Loading\nExplanation of complex parameters below:\n* .CSV File: Upload the .csv file according to the template shown here. Any well to the left of a forward slash (/) will correspond to the well in the reservoir containing the desired target cell. Any well to the right of a forward slash (/) will correspond to the effector cell in the 96 well plate for part 2 of this protocol. If a cell is only to receive one of the effector or target cells, place a 0 (e.g. A1/0 would mean target cell from A1 of the reservoir with no effector cell). All cells that are to be skipped (receive neither effector nor target cell) should have a lowercase 'x' in the resepective cell in the .csv file. For the parameters below, make sure there are NO commas inside of the wells, and just the values. For the mount, put nothing else but \"left\" or \"right\". For the pre-mix variable, you must start the well with \"Yes\" or \"No\", but can put anything else after that (e.g. \"Yes premix\", or \"No premix\").\n* Transfer Volume Target Cell: Specify the volume (in ul) to transfer between target cells in reservoir to well plate.\n* Pre-mix before aspirating in source reservoir?: Specify whether or not to pre-mix before each transfer of target cell in reservoir to plate.\n* Pre-mix height in reservoir: If Pre-mix variable is set to Yes, specify the height in the reservoir wells in which to pre-mix.\n* Pre-mix repetitions: If Pre-mix variable is set to Yes, specify the number of repetitions to mix before each transfer.\n* Pre-mix Volume: If Pre-mix variable is set to Yes, specify the pre-mix volume (in ul).\n* Pre-mix Rate: If Pre-mix variable is set to Yes, specify the mix rate. A value of 1 is default mix speed, whereas a value of 0.5 is half of the default mix speed, etc.\n* Dispense Reservoir Height: Specify the height above the reservoir bottom to dispense residual solution.\n* Transfer Aspiration Height: Specify the height in which to aspirate from in the reservoir. Default is 1mm from the bottom of the reservoir.\n* Transfer Dispense Height: Specify the height in which to dispense from in the well plate. Default is 1mm from the bottom of the reservoir.\n* Aspiration Rate: Specify the aspiration rate for transfers. A value of 1 is default aspiration speed, whereas a value of 0.5 is half of the default aspiration speed, etc.\n* Dispense Rate: Specify the dispense rate for transfers. A value of 1 is default dispense speed, whereas a value of 0.5 is half of the default dispense speed, etc.\n* P300 Multi-Channel Mount: Specify whether the P300 Multi-Channel pipette is on the left or right mount.\n", + "description": "This protocol parses an uploaded .csv file (see below) and determines the number of tips to pick up with a multi-channel pipette. The pipette transfers the specified volume of effector cell to a 384 well-plate to the parsed wells by multi-dispensing as much as the pipette tip can accommodate before returning to the reservoir. The pipette keeps the same tip for the duration of the run.\nNote: Part 1 and Part 2 should receive the exact same .csv file.\nFind part one of the protocol (target cell loading) below:\nPart 1 - Target Cell Loading\nExplanation of complex parameters below:\n .CSV File: Upload the .csv file according to the template shown here. Any well to the left of a forward slash (/) will correspond to the well in the reservoir containing the desired target cell. Any well to the right of a forward slash (/) will correspond to the effector cell in the 96 well plate for part 2 of this protocol. If a cell is only to receive one of the effector or target cells, place a 0 (e.g. A1/0 would mean target cell from A1 of the reservoir with no effector cell). All cells that are to be skipped (receive neither effector nor target cell) should have a lowercase 'x' in the resepective cell in the .csv file. For the parameters below, make sure there are NO commas inside of the wells, and just the values. For the mount, put nothing else but \"left\" or \"right\". For the pre-mix variable, you must start the well with \"Yes\" or \"No\", but can put anything else after that (e.g. \"Yes premix\", or \"No premix\").\n Transfer Volume Target Cell: Specify the volume (in ul) to transfer between target cells in reservoir to well plate.\n Pre-mix before aspirating in source reservoir?: Specify whether or not to pre-mix before each transfer of target cell in reservoir to plate.\n Pre-mix height in reservoir: If Pre-mix variable is set to Yes, specify the height in the reservoir wells in which to pre-mix.\n Pre-mix repetitions: If Pre-mix variable is set to Yes, specify the number of repetitions to mix before each transfer.\n Pre-mix Volume: If Pre-mix variable is set to Yes, specify the pre-mix volume (in ul).\n Pre-mix Rate: If Pre-mix variable is set to Yes, specify the mix rate. A value of 1 is default mix speed, whereas a value of 0.5 is half of the default mix speed, etc.\n Dispense Reservoir Height: Specify the height above the reservoir bottom to dispense residual solution.\n Transfer Aspiration Height: Specify the height in which to aspirate from in the reservoir. Default is 1mm from the bottom of the reservoir.\n Transfer Dispense Height: Specify the height in which to dispense from in the well plate. Default is 1mm from the bottom of the reservoir.\n Aspiration Rate: Specify the aspiration rate for transfers. A value of 1 is default aspiration speed, whereas a value of 0.5 is half of the default aspiration speed, etc.\n Dispense Rate: Specify the dispense rate for transfers. A value of 1 is default dispense speed, whereas a value of 0.5 is half of the default dispense speed, etc.\n* P300 Multi-Channel Mount: Specify whether the P300 Multi-Channel pipette is on the left or right mount.\n", "internal": "581011", "labware": "\nCorning 384 Well Plate 112 \u00b5L Flat\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 200uL Filter Tips\n", "markdown": { diff --git a/protoBuilds/581011/README.json b/protoBuilds/581011/README.json index cdfe915fa..77be64fb7 100644 --- a/protoBuilds/581011/README.json +++ b/protoBuilds/581011/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck layout with 6 target cells in the reservoir on Slot 5.\n\n\n", - "description": "This protocol parses an uploaded .csv file (see below) and determines the number of tips to pick up with a multi-channel pipette. The pipette transfers the specified volume of target cell to a 384 well-plate to the parsed wells by multi-dispensing as much as the pipette tip can accommodate before returning to the reservoir. New tips are awarded between each target cell.\nNote: Part 1 and Part 2 should receive the exact same .csv file.\nFind part two of the protocol (effector cell loading) below:\nPart 2 - Effector Cell Loading\nExplanation of complex parameters below:\n* .CSV File: Upload the .csv file according to the template shown here. Any well to the left of a forward slash (/) will correspond to the well in the reservoir containing the desired target cell. Any well to the right of a forward slash (/) will correspond to the effector cell in the 96 well plate for part 2 of this protocol. If a cell is only to receive one of the effector or target cells, place a 0 (e.g. A1/0 would mean target cell from A1 of the reservoir with no effector cell). All cells that are to be skipped (receive neither effector nor target cell) should have a lowercase 'x' in the resepective cell in the .csv file. For the parameters below, make sure there are NO commas inside of the wells, and just the values. For the mount, put nothing else but \"left\" or \"right\". For the pre-mix variable, you must start the well with \"Yes\" or \"No\", but can put anything else after that (e.g. \"Yes premix\", or \"No premix\").\n* Transfer Volume Effector Cell: Specify the volume (in ul) to transfer between effector cells in reservoir to well plate.\n* Pre-mix before aspirating in source well plate?: Specify whether or not to pre-mix before each transfer of target cell in reservoir to plate.\n* Pre-mix height in well plate: If Pre-mix variable is set to Yes, specify the height in the reservoir wells in which to pre-mix.\n* Pre-mix repetitions: If Pre-mix variable is set to Yes, specify the number of repetitions to mix before each transfer.\n* Pre-mix Volume: If Pre-mix variable is set to Yes, specify the pre-mix volume (in ul).\n* Pre-mix Rate: If Pre-mix variable is set to Yes, specify the mix rate. A value of 1 is default mix speed, whereas a value of 0.5 is half of the default mix speed, etc.\n* Dispense Reservoir Height: Specify the height above the reservoir bottom to dispense residual solution.\n* Transfer Aspiration/Dispense Height: Specify the height in which to aspirate/dispense from in the well plate. Default is 1mm from the bottom of the reservoir.\n* Transfer Dispense Height: Specify the height in which to dispense from in the well plate. Default is 1mm from the bottom of the reservoir.\n* Aspiration Rate: Specify the aspiration rate for transfers. A value of 1 is default aspiration speed, whereas a value of 0.5 is half of the default aspiration speed, etc.\n* Dispense Rate: Specify the dispense rate for transfers. A value of 1 is default dispense speed, whereas a value of 0.5 is half of the default dispense speed, etc.\n* P300 Multi-Channel Mount: Specify whether the P300 Multi-Channel pipette is on the left or right mount.\n", + "description": "This protocol parses an uploaded .csv file (see below) and determines the number of tips to pick up with a multi-channel pipette. The pipette transfers the specified volume of target cell to a 384 well-plate to the parsed wells by multi-dispensing as much as the pipette tip can accommodate before returning to the reservoir. New tips are awarded between each target cell.\nNote: Part 1 and Part 2 should receive the exact same .csv file.\nFind part two of the protocol (effector cell loading) below:\nPart 2 - Effector Cell Loading\nExplanation of complex parameters below:\n .CSV File: Upload the .csv file according to the template shown here. Any well to the left of a forward slash (/) will correspond to the well in the reservoir containing the desired target cell. Any well to the right of a forward slash (/) will correspond to the effector cell in the 96 well plate for part 2 of this protocol. If a cell is only to receive one of the effector or target cells, place a 0 (e.g. A1/0 would mean target cell from A1 of the reservoir with no effector cell). All cells that are to be skipped (receive neither effector nor target cell) should have a lowercase 'x' in the resepective cell in the .csv file. For the parameters below, make sure there are NO commas inside of the wells, and just the values. For the mount, put nothing else but \"left\" or \"right\". For the pre-mix variable, you must start the well with \"Yes\" or \"No\", but can put anything else after that (e.g. \"Yes premix\", or \"No premix\").\n Transfer Volume Effector Cell: Specify the volume (in ul) to transfer between effector cells in reservoir to well plate.\n Pre-mix before aspirating in source well plate?: Specify whether or not to pre-mix before each transfer of target cell in reservoir to plate.\n Pre-mix height in well plate: If Pre-mix variable is set to Yes, specify the height in the reservoir wells in which to pre-mix.\n Pre-mix repetitions: If Pre-mix variable is set to Yes, specify the number of repetitions to mix before each transfer.\n Pre-mix Volume: If Pre-mix variable is set to Yes, specify the pre-mix volume (in ul).\n Pre-mix Rate: If Pre-mix variable is set to Yes, specify the mix rate. A value of 1 is default mix speed, whereas a value of 0.5 is half of the default mix speed, etc.\n Dispense Reservoir Height: Specify the height above the reservoir bottom to dispense residual solution.\n Transfer Aspiration/Dispense Height: Specify the height in which to aspirate/dispense from in the well plate. Default is 1mm from the bottom of the reservoir.\n Transfer Dispense Height: Specify the height in which to dispense from in the well plate. Default is 1mm from the bottom of the reservoir.\n Aspiration Rate: Specify the aspiration rate for transfers. A value of 1 is default aspiration speed, whereas a value of 0.5 is half of the default aspiration speed, etc.\n Dispense Rate: Specify the dispense rate for transfers. A value of 1 is default dispense speed, whereas a value of 0.5 is half of the default dispense speed, etc.\n* P300 Multi-Channel Mount: Specify whether the P300 Multi-Channel pipette is on the left or right mount.\n", "internal": "581011", "labware": "\nCorning 384 Well Plate 112 \u00b5L Flat\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 200uL Filter Tips\n", "markdown": { diff --git a/protoBuilds/5829d7/README.json b/protoBuilds/5829d7/README.json index 5f5c2df58..33108d00f 100644 --- a/protoBuilds/5829d7/README.json +++ b/protoBuilds/5829d7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck layout with example 90 tubes. Note: tubes should be placed by row in the tube racks, starting from the tube rack in slot 1. Tubes are transferred 1-1 with well plate wells by row.\n\n\n", - "description": "200ul of viral transport media (VTM) is reformatted from (up to) 96 tubes split amongst 3 tube racks to a 96 well plate. Tubes are reformatted by row in tube racks 1 (slot 1), 2 (slot 4), and then 3 (slot 7).\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples for this run.\n* Tube Aspiration Height: Specify the aspiration height in the tubes. Default is 1mm.\n* Well Dispense Height: Specify the dispense height in the wells. Default is 1mm.\n* Aspirate/Dispense Flow rate: Specify the aspirate/dispense flow rate in the wells. Default is 274ul/sec.\n* P1000 Single-Channel Mount: Specify (left) or (right) mount for the P1000 single channel pipette.\n", + "description": "200ul of viral transport media (VTM) is reformatted from (up to) 96 tubes split amongst 3 tube racks to a 96 well plate. Tubes are reformatted by row in tube racks 1 (slot 1), 2 (slot 4), and then 3 (slot 7).\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples for this run.\n Tube Aspiration Height: Specify the aspiration height in the tubes. Default is 1mm.\n Well Dispense Height: Specify the dispense height in the wells. Default is 1mm.\n Aspirate/Dispense Flow rate: Specify the aspirate/dispense flow rate in the wells. Default is 274ul/sec.\n* P1000 Single-Channel Mount: Specify (left) or (right) mount for the P1000 single channel pipette.\n", "internal": "5829d7", "labware": "\nOpentrons 1000uL Filter Tips\nQiagen 96 Well plate\n(3) Custom Opentrons 32-tube tube racks.\n", "markdown": { diff --git a/protoBuilds/58d57d/README.json b/protoBuilds/58d57d/README.json index 47afba5ae..c7d1ed458 100644 --- a/protoBuilds/58d57d/README.json +++ b/protoBuilds/58d57d/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol performs transfers of reagents for the Promega ADP-Glo Kinase Assay. It will transfer four different liquids into the test wells with pauses for centrifugation and incubations in between transfers.\n\n\n\nP20 single-channel GEN2 electronic pipette\nGreiner Microplate 384 Wells\n\n\n\nDeck Setup\n* Greiner 384 Well Plate (Slot 1)\n* Opentrons 20uL Tips (Slot 2)\n* Opentrons 24 Tube Rack 1.5mL Tubes (Slot 4)\nReagent Setup: Opentrons 24 Tube Rack 1.5mL Tubes (Slot 4):\n* Liquid A (A1)\n* Liquid B (B1)\n* Liquid C (C1)\n* Liquid D (D1)", + "description": "This protocol performs transfers of reagents for the Promega ADP-Glo Kinase Assay. It will transfer four different liquids into the test wells with pauses for centrifugation and incubations in between transfers.\n\n\n\nP20 single-channel GEN2 electronic pipette\nGreiner Microplate 384 Wells\n\n\n\nDeck Setup\n Greiner 384 Well Plate (Slot 1)\n Opentrons 20uL Tips (Slot 2)\n* Opentrons 24 Tube Rack 1.5mL Tubes (Slot 4)\nReagent Setup: Opentrons 24 Tube Rack 1.5mL Tubes (Slot 4):\n Liquid A (A1)\n Liquid B (B1)\n Liquid C (C1)\n Liquid D (D1)", "internal": "58d57d", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/5b16ef-pt2/README.json b/protoBuilds/5b16ef-pt2/README.json index ab74d29e8..7d7ca0868 100644 --- a/protoBuilds/5b16ef-pt2/README.json +++ b/protoBuilds/5b16ef-pt2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Note: Split the ethanol evenly in columns 11 and 12 of the reservoir if running 5 or 6 columns of samples. If running 4 or fewer columns of samples, place all the ethanol in column 11 of the reservoir exclusively.\n", - "description": "This protocol is a semi-automated workflow which performs 8.1-8.4.6 of the SARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB kit. For detailed information on protocol steps, please see below. You can find part 1 of the protocol here:\n\nSARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB - Part 1\n\nExplanation of complex parameters below:\n* Number of Sample Columns (1-6): Specify how many sample columns (1-6) this run will process. Samples will be placed in every other column, starting from column 1 (i.e. 1, 3, 5, 7, 9, 11 for 6 columns).\n* csv: csv should be formatted in the following order, including the header line (also be sure to skip columns):\nWell, DNA Volume (ul), Pool Volume\nA1, 5, 5\nB1, 3, 5\nC1, 5, 5\nD1, 5, 5\nE1, 2, 5\nF1, 5, 5\nG1, 5, 5\nH1, 4, 5\nA3, 5, 5\n* Index Start Column (1-12): Specify which column in the index plate to begin aspirating from. Note: the number of index columns left should be greater or equal to the number of sample columns. If not, the protocol will throw an error at the beginning of the run.\n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 and P300 multi-channel pipettes.\n", + "description": "This protocol is a semi-automated workflow which performs 8.1-8.4.6 of the SARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB kit. For detailed information on protocol steps, please see below. You can find part 1 of the protocol here:\n\nSARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB - Part 1\n\nExplanation of complex parameters below:\n Number of Sample Columns (1-6): Specify how many sample columns (1-6) this run will process. Samples will be placed in every other column, starting from column 1 (i.e. 1, 3, 5, 7, 9, 11 for 6 columns).\n csv: csv should be formatted in the following order, including the header line (also be sure to skip columns):\nWell, DNA Volume (ul), Pool Volume\nA1, 5, 5\nB1, 3, 5\nC1, 5, 5\nD1, 5, 5\nE1, 2, 5\nF1, 5, 5\nG1, 5, 5\nH1, 4, 5\nA3, 5, 5\n Index Start Column (1-12): Specify which column in the index plate to begin aspirating from. Note: the number of index columns left should be greater or equal to the number of sample columns. If not, the protocol will throw an error at the beginning of the run.\n P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 and P300 multi-channel pipettes.\n", "internal": "5b16ef-pt2", "labware": "\nNEST 12 well reservoir 15mL\nNEST 1 well reservoir 195mL\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons 20ul Tips\nOpentrons 300ul Tips\nNEST 12 well reservoir 195mL\nIndex Plate\n", "markdown": { diff --git a/protoBuilds/5b16ef/README.json b/protoBuilds/5b16ef/README.json index 6069b6b2b..d4321a687 100644 --- a/protoBuilds/5b16ef/README.json +++ b/protoBuilds/5b16ef/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol is a semi-automated workflow which performs 8.1-8.4.6 of the SARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB kit. For detailed information on protocol steps, please see below. You can find part 2 of the protocol here:\n\nSARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB - Part 2\n\nExplanation of complex parameters below:\n* Number of Sample Columns (1-6): Specify how many sample columns (1-6) this run will process. Samples will be placed in every other column, starting from column 1 (i.e. 1, 3, 5, 7, 9, 11 for 6 columns).\n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 pipette.\n", + "description": "This protocol is a semi-automated workflow which performs 8.1-8.4.6 of the SARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB kit. For detailed information on protocol steps, please see below. You can find part 2 of the protocol here:\n\nSARS-CoV-2 Using Illumina Nextera Flex & MiSeqNEB - Part 2\n\nExplanation of complex parameters below:\n Number of Sample Columns (1-6): Specify how many sample columns (1-6) this run will process. Samples will be placed in every other column, starting from column 1 (i.e. 1, 3, 5, 7, 9, 11 for 6 columns).\n P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 pipette.\n", "internal": "5b16ef", "labware": "\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nOpentrons 20ul Tips\n", "markdown": { diff --git a/protoBuilds/5b8174/README.json b/protoBuilds/5b8174/README.json index a01492814..d880e2eb5 100644 --- a/protoBuilds/5b8174/README.json +++ b/protoBuilds/5b8174/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nIf the deck layout of a particular protocol is more or less static, it is often helpful to attach a preview of the deck layout, most descriptively generated with Labware Creator. Example:\n\n\n", - "description": "This protocol performs transfers of positive controls and patient samples to a 384 well plate loaded onto a temperature module. All labware and transfers can be controlled through the CSV files that are used as input for this protocol.\nExplanation of complex parameters below:\n* P20 Single Channel Pipette Mount Position: Choose the mount position of your pipette.\n* Control CSV File: Upload the CSV file for controls here. You can download an example CSV file here OR follow the format directly below. Note: The control source slot and destination slot are converted from the Eppendorf Rack format to the Opentrons 24 Tube Rack Format. Please refer to the Control Conversion Table at the end of this section.\nRack,Sr.Barcode,,Dest.Barcode,Dest.List Name,\n1,,PCRCTR15000004,,,\n2,,,,,\n3,,,,,\n4,,,,,\n,,,,,\nSource Labware,Source Slot,Source Well,Dest Labware,Dest Slot,Dest Well\neppendorf_24_tuberack_generic_2.0ml_screwcap,1,D2,appliedbiosystems_384_wellplate_20ul,9,B1\neppendorf_24_tuberack_generic_2.0ml_screwcap,1,D3,appliedbiosystems_384_wellplate_20ul,9,A4\neppendorf_24_tuberack_generic_2.0ml_screwcap,1,D4,appliedbiosystems_384_wellplate_20ul,9,D2\n* Assembly CSV File: Upload the CSV file for assembly/patient samples here. You can download an example CSV file here OR follow the format directly below.\nRack,Sr.Barcode, ,Dest.Barcode,Dest.List Name,\n1,,,,,\n2,,,,,\n3,,,,,\n4,,,,,\n,,,,,\nSource Labware,Source Slot,Source Well,Dest Labware,Dest Slot,Dest Well\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,C11,appliedbiosystems_384_wellplate_20ul,6,B1\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,E11,appliedbiosystems_384_wellplate_20ul,6,A4\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,E11,appliedbiosystems_384_wellplate_20ul,6,D2\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,E11,appliedbiosystems_384_wellplate_20ul,6,E2\n* 96 Well Plates Aspiration Height (mm): The aspiration height from the bottom of the well when aspirating from the assembly 96 well plates.\nControl Conversion Table\nEppendorf Source Well, Destination Slot, Destination Well\nA1,10,A1\nA2,10,A2\nA3,10,A3\nA4,10,A4\nA5,10,A5\nA6,10,A6\nB1,10,B1\nB2,10,B2\nB3,10,B3\nB4,10,B4\nB5,10,B5\nB6,10,B6\nC1,10,C1\nC2,10,C2\nC3,10,C3\nC4,10,C4\nC5,10,C5\nC6,10,C6\nD1,10,D1\nD2,10,D2\nD3,10,D3\nD4,10,D4\nD5,10,D5\nD6,10,D6\nE1,7,A1\nE2,7,A2\nE3,7,A3\nE4,7,A4\nE5,7,A5\nE6,7,A6\nF1,7,B1\nF2,7,B2\nF3,7,B3\nF4,7,B4\nF5,7,B5\nF6,7,B6\nG1,7,C1\nG2,7,C2\nG3,7,C3\nG4,7,C4\nG5,7,C5\nG6,7,C6\nH1,7,D1\nH2,7,D2\nH3,7,D3\nH4,7,D4\nH5,7,D5\nH6,7,D6\nI1,4,A1\nI2,4,A2\nI3,4,A3\nI4,4,A4\nI5,4,A5\nI6,4,A6\nJ1,4,B1\nJ2,4,B2\nJ3,4,B3\nJ4,4,B4\nJ5,4,B5\nJ6,4,B6\nK1,4,C1\nK2,4,C2\nK3,4,C3\nK4,4,C4\nK5,4,C5\nK6,4,C6\nL1,4,D1\nL2,4,D2\nL3,4,D3\nL4,4,D4\nL5,4,D5\nL6,4,D6\n", + "description": "This protocol performs transfers of positive controls and patient samples to a 384 well plate loaded onto a temperature module. All labware and transfers can be controlled through the CSV files that are used as input for this protocol.\nExplanation of complex parameters below:\n P20 Single Channel Pipette Mount Position: Choose the mount position of your pipette.\n Control CSV File: Upload the CSV file for controls here. You can download an example CSV file here OR follow the format directly below. Note: The control source slot and destination slot are converted from the Eppendorf Rack format to the Opentrons 24 Tube Rack Format. Please refer to the Control Conversion Table at the end of this section.\nRack,Sr.Barcode,,Dest.Barcode,Dest.List Name,\n1,,PCRCTR15000004,,,\n2,,,,,\n3,,,,,\n4,,,,,\n,,,,,\nSource Labware,Source Slot,Source Well,Dest Labware,Dest Slot,Dest Well\neppendorf_24_tuberack_generic_2.0ml_screwcap,1,D2,appliedbiosystems_384_wellplate_20ul,9,B1\neppendorf_24_tuberack_generic_2.0ml_screwcap,1,D3,appliedbiosystems_384_wellplate_20ul,9,A4\neppendorf_24_tuberack_generic_2.0ml_screwcap,1,D4,appliedbiosystems_384_wellplate_20ul,9,D2\n Assembly CSV File: Upload the CSV file for assembly/patient samples here. You can download an example CSV file here OR follow the format directly below.\nRack,Sr.Barcode, ,Dest.Barcode,Dest.List Name,\n1,,,,,\n2,,,,,\n3,,,,,\n4,,,,,\n,,,,,\nSource Labware,Source Slot,Source Well,Dest Labware,Dest Slot,Dest Well\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,C11,appliedbiosystems_384_wellplate_20ul,6,B1\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,E11,appliedbiosystems_384_wellplate_20ul,6,A4\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,E11,appliedbiosystems_384_wellplate_20ul,6,D2\nappliedbiosystems_96_wellplate_200ul_on_eppendorf_cooling_block,2,E11,appliedbiosystems_384_wellplate_20ul,6,E2\n 96 Well Plates Aspiration Height (mm): The aspiration height from the bottom of the well when aspirating from the assembly 96 well plates.\nControl Conversion Table\nEppendorf Source Well, Destination Slot, Destination Well\nA1,10,A1\nA2,10,A2\nA3,10,A3\nA4,10,A4\nA5,10,A5\nA6,10,A6\nB1,10,B1\nB2,10,B2\nB3,10,B3\nB4,10,B4\nB5,10,B5\nB6,10,B6\nC1,10,C1\nC2,10,C2\nC3,10,C3\nC4,10,C4\nC5,10,C5\nC6,10,C6\nD1,10,D1\nD2,10,D2\nD3,10,D3\nD4,10,D4\nD5,10,D5\nD6,10,D6\nE1,7,A1\nE2,7,A2\nE3,7,A3\nE4,7,A4\nE5,7,A5\nE6,7,A6\nF1,7,B1\nF2,7,B2\nF3,7,B3\nF4,7,B4\nF5,7,B5\nF6,7,B6\nG1,7,C1\nG2,7,C2\nG3,7,C3\nG4,7,C4\nG5,7,C5\nG6,7,C6\nH1,7,D1\nH2,7,D2\nH3,7,D3\nH4,7,D4\nH5,7,D5\nH6,7,D6\nI1,4,A1\nI2,4,A2\nI3,4,A3\nI4,4,A4\nI5,4,A5\nI6,4,A6\nJ1,4,B1\nJ2,4,B2\nJ3,4,B3\nJ4,4,B4\nJ5,4,B5\nJ6,4,B6\nK1,4,C1\nK2,4,C2\nK3,4,C3\nK4,4,C4\nK5,4,C5\nK6,4,C6\nL1,4,D1\nL2,4,D2\nL3,4,D3\nL4,4,D4\nL5,4,D5\nL6,4,D6\n", "internal": "5b8174", "labware": "\nOpentrons 20 uL Tips\n", "markdown": { diff --git a/protoBuilds/5c14ad/README.json b/protoBuilds/5c14ad/README.json index ec7850c71..6d65473a9 100644 --- a/protoBuilds/5c14ad/README.json +++ b/protoBuilds/5c14ad/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol allows the user to fill custom adapters according to their specifications (found below):\nThe user can choose between: Salmonella or Listeria Fill (90\u00b5L, 70\u00b5L respectively), how many plates to fill (1-9), single channel or multi-channel pipette (P300), and which column to pick up a tip from (row A, to avoid cross contamination).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single Channel Pipette, or\nP300 Multi Channel Pipette\nFisherbrand 20-200\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\nNest 195mL Reservoir (or similar)\n\n\n\nFor this protocol, be sure that the correct Lysis Type is selected for correct volume transfers, as well as Pipette Type and Mount.\nLabware Setup\nSlot 1: Fisherbrand 20-200\u00b5L Tips\nSlot 2: Nest Reservoir\nSlot 3 - 11 (loaded sequentially): Simport Scientific 500\u00b5L Tubes in Custom Holder\nUsing the customization fields below, set up your protocol.\n* Lysis Type (Salmonella/Listeria): Select either Salmonella or Listeria and the corresponding volume (90\u00b5L or 70\u00b5L, respectively) will be added to each well.\n* Pipette Type: Select either Single Channel or Multi Channel. This will also modify the protocol behavior to the corresponding protocol.\n* Pipette Mount: Specify which mount the P300 is on (left or right).\n* Number of Plates: Specify how many plates to fill (1-9).\n* Tip Pick-Up at (Row A): Specify which column to pick up tip (1-12).\n", + "description": "This protocol allows the user to fill custom adapters according to their specifications (found below):\nThe user can choose between: Salmonella or Listeria Fill (90\u00b5L, 70\u00b5L respectively), how many plates to fill (1-9), single channel or multi-channel pipette (P300), and which column to pick up a tip from (row A, to avoid cross contamination).\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP300 Single Channel Pipette, or\nP300 Multi Channel Pipette\nFisherbrand 20-200\u00b5L Tips\nSimport Scientific 500\u00b5L Tubes in Custom Holder\nNest 195mL Reservoir (or similar)\n\n\n\nFor this protocol, be sure that the correct Lysis Type is selected for correct volume transfers, as well as Pipette Type and Mount.\nLabware Setup\nSlot 1: Fisherbrand 20-200\u00b5L Tips\nSlot 2: Nest Reservoir\nSlot 3 - 11 (loaded sequentially): Simport Scientific 500\u00b5L Tubes in Custom Holder\nUsing the customization fields below, set up your protocol.\n Lysis Type (Salmonella/Listeria): Select either Salmonella or Listeria and the corresponding volume (90\u00b5L or 70\u00b5L, respectively) will be added to each well.\n Pipette Type: Select either Single Channel or Multi Channel. This will also modify the protocol behavior to the corresponding protocol.\n Pipette Mount: Specify which mount the P300 is on (left or right).\n Number of Plates: Specify how many plates to fill (1-9).\n* Tip Pick-Up at (Row A): Specify which column to pick up tip (1-12).\n", "internal": "5c14ad", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/5c24e2/README.json b/protoBuilds/5c24e2/README.json index a95dd7cd7..080a8fe35 100644 --- a/protoBuilds/5c24e2/README.json +++ b/protoBuilds/5c24e2/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol transfers sample from NEST 96-Well Plates to Applied Biosystems MicroAmp 384-well plates with mastermix. Update: this protocol has been updated to accommodate the SSI 384-well plate as well.\n\nThe protocol can fill one or two, 384-well plates. The P20 Single-Channel Pipette will aspirate 5\u00b5L from each well of the NEST 96-Well Plates and dispense 2.5\u00b5L into two wells of the (A1 --> A1/B1; B1 --> C1/D1; etc.)\n\nUpdate (10/22/20): The protocol will now aspirate 10\u00b5L and dispense 5\u00b5L into two wells.\n\nUpdate (11/2/20): The protocol will now aspirate 20\u00b5L and dispense 10\u00b5L into two wells. Additionally, the option to use the p300-multi pipette has been added.\nUpdated (11/12/20): A new parameter has been added that allows the user to input the volume (in \u00b5L) of sample that should be transferred. The pipette will aspirate 2x the volume and dispense into two wells.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P20 Single-Channel Pipette\nOpentrons 20\u00b5L Tips\nApplied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate with mastermix\nNEST 96-Well Plates with samples\n\n\n\nSlots 1: Opentrons 20\u00b5L Tips\nSlot 2: NEST 96-Well Plates with samples\nSlot 3: Applied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate with mastermix\nSlot 4: Opentrons 20\u00b5L Tips\nSlot 5: NEST 96-Well Plates with samples\nSlot 6: Applied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate with mastermix (if filling two plates)\nSlot 7: Opentrons 20\u00b5L Tips (if filling two plates)\nSlot 8: NEST 96-Well Plates with samples (if filling two plates)\nSlot 9: empty\nSlot 10: Opentrons 20\u00b5L Tips (if filling two plates)\nSlot 11: NEST 96-Well Plates with samples (if filling two plates)\n\n\nUsing the customizations field (below), set up your protocol.\n* Pipette Type: Select which pipette will be used\n* Pipette Mount: Select which mount (left or right) the pipette is attached to.\n* Sample Volume (uL): Input the sample volume\n* How many 384-well plates: Specify the number of 384-well plates to fill\n* Plate (384-Well) Type: Specify the type of 384-well plates that are being used", + "description": "This protocol transfers sample from NEST 96-Well Plates to Applied Biosystems MicroAmp 384-well plates with mastermix. Update: this protocol has been updated to accommodate the SSI 384-well plate as well.\n\nThe protocol can fill one or two, 384-well plates. The P20 Single-Channel Pipette will aspirate 5\u00b5L from each well of the NEST 96-Well Plates and dispense 2.5\u00b5L into two wells of the (A1 --> A1/B1; B1 --> C1/D1; etc.)\n\nUpdate (10/22/20): The protocol will now aspirate 10\u00b5L and dispense 5\u00b5L into two wells.\n\nUpdate (11/2/20): The protocol will now aspirate 20\u00b5L and dispense 10\u00b5L into two wells. Additionally, the option to use the p300-multi pipette has been added.\nUpdated (11/12/20): A new parameter has been added that allows the user to input the volume (in \u00b5L) of sample that should be transferred. The pipette will aspirate 2x the volume and dispense into two wells.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P20 Single-Channel Pipette\nOpentrons 20\u00b5L Tips\nApplied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate with mastermix\nNEST 96-Well Plates with samples\n\n\n\nSlots 1: Opentrons 20\u00b5L Tips\nSlot 2: NEST 96-Well Plates with samples\nSlot 3: Applied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate with mastermix\nSlot 4: Opentrons 20\u00b5L Tips\nSlot 5: NEST 96-Well Plates with samples\nSlot 6: Applied Biosystems MicroAmp 384-Well Plate or SSI 384-Well Plate with mastermix (if filling two plates)\nSlot 7: Opentrons 20\u00b5L Tips (if filling two plates)\nSlot 8: NEST 96-Well Plates with samples (if filling two plates)\nSlot 9: empty\nSlot 10: Opentrons 20\u00b5L Tips (if filling two plates)\nSlot 11: NEST 96-Well Plates with samples (if filling two plates)\n\n\nUsing the customizations field (below), set up your protocol.\n Pipette Type: Select which pipette will be used\n Pipette Mount: Select which mount (left or right) the pipette is attached to.\n Sample Volume (uL): Input the sample volume\n How many 384-well plates: Specify the number of 384-well plates to fill\n* Plate (384-Well) Type: Specify the type of 384-well plates that are being used", "internal": "5c24e2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/5c50d9/README.json b/protoBuilds/5c50d9/README.json index 421152335..bb692af8e 100644 --- a/protoBuilds/5c50d9/README.json +++ b/protoBuilds/5c50d9/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck map with lysis buffer in A1 (first well) of the Nest 12 well reservoir.\n\n\n", - "description": "This protocol first preps one 384 well plate with lysis buffer and sample to undergo a thermocycler. In this step, samples are transferred from tube rack to the 384 well plate. If the number of samples selected exceeds the number of samples that can fit onto the deck, the protocol pauses and prompts the user to refill the tube racks with new samples up to the number of samples selected. Afterwards, 4ul of the resulting solution is transferred to the final 384 well plate.\nExplanation of complex parameters below:\n* Number of Samples: Select the number of samples (1-384) for this run. If larger than 90 samples are selected, the protocol will pause after the last sample is transferred on the deck and will prompt the user to refill samples up to the number specified. Samples should always be placed in the tuberack down by column, and in the order of the deck slots (i.e. 4, 5, 6 ..., etc.)\n* P20/P300 Dispense Flow Rate: Global control of P20 and P300 dispense flow rate. A value of 1.0 is default, 0.5 is 50% of the default flow rate, 1.2 is 20% faster the default flow rate, etc. \n* P20 Single Mount: Specify whether the P20 single channel pipette will be mounted on the left or right.\n* P300 Single Mount: Specify whether the P300 single channel pipette will be mounted on the left or right.\n", + "description": "This protocol first preps one 384 well plate with lysis buffer and sample to undergo a thermocycler. In this step, samples are transferred from tube rack to the 384 well plate. If the number of samples selected exceeds the number of samples that can fit onto the deck, the protocol pauses and prompts the user to refill the tube racks with new samples up to the number of samples selected. Afterwards, 4ul of the resulting solution is transferred to the final 384 well plate.\nExplanation of complex parameters below:\n Number of Samples: Select the number of samples (1-384) for this run. If larger than 90 samples are selected, the protocol will pause after the last sample is transferred on the deck and will prompt the user to refill samples up to the number specified. Samples should always be placed in the tuberack down by column, and in the order of the deck slots (i.e. 4, 5, 6 ..., etc.)\n P20/P300 Dispense Flow Rate: Global control of P20 and P300 dispense flow rate. A value of 1.0 is default, 0.5 is 50% of the default flow rate, 1.2 is 20% faster the default flow rate, etc. \n P20 Single Mount: Specify whether the P20 single channel pipette will be mounted on the left or right.\n P300 Single Mount: Specify whether the P300 single channel pipette will be mounted on the left or right.\n", "internal": "5c50d9", "labware": "\nCustom 384 well plate\nOpentrons 4-in-1 tube rack with 15 tube insert\nOpentrons 200ul filter tips\nOpentrons 20ul tips\nNest 12 Well Reservoir, 195mL\n", "markdown": { diff --git a/protoBuilds/5c7384/README.json b/protoBuilds/5c7384/README.json index 0d7ad0989..d3378c35f 100644 --- a/protoBuilds/5c7384/README.json +++ b/protoBuilds/5c7384/README.json @@ -5,7 +5,7 @@ "Mass Spec" ] }, - "description": "This protocol performs mass spec sample prep per this SP3 Proteomics manual (Appendix Protocol B). The following steps are performed throughout the protocol with the use of the Opentrons OT-2, Thermocycler Module, and Magnetic Module (GEN2):\n\nReduction and Alkylation\nProtein Binding\nEthanol Wash\nAcetonitrile Wash\nOn-Bead Digestion\n\nDue to limited deck space, the user is prompted to change tipracks on the deck when needed, and to move labware when needed.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0 or later)\nOpentrons P20 GEN2 Single-Channel Pipette\nOpentrons 20\u00b5L Tips\nOpentrons P300 GEN2 Single-Channel Pipette\nOpentrons 300\u00b5L Tips\nNEST 96-Well Plates or comparable PCR plates\n\n\n\nReagent plate (slot 5):\n* column 1: DTT\n* column 2: CAA\n* column 3: magnetic bead stock\n* columns 4-5: ABC\n* column 6: trypsin\nEthanol plate (slot 2)\nAcetonitrile plate (slot 3)", + "description": "This protocol performs mass spec sample prep per this SP3 Proteomics manual (Appendix Protocol B). The following steps are performed throughout the protocol with the use of the Opentrons OT-2, Thermocycler Module, and Magnetic Module (GEN2):\n\nReduction and Alkylation\nProtein Binding\nEthanol Wash\nAcetonitrile Wash\nOn-Bead Digestion\n\nDue to limited deck space, the user is prompted to change tipracks on the deck when needed, and to move labware when needed.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0 or later)\nOpentrons P20 GEN2 Single-Channel Pipette\nOpentrons 20\u00b5L Tips\nOpentrons P300 GEN2 Single-Channel Pipette\nOpentrons 300\u00b5L Tips\nNEST 96-Well Plates or comparable PCR plates\n\n\n\nReagent plate (slot 5):\n column 1: DTT\n column 2: CAA\n column 3: magnetic bead stock\n columns 4-5: ABC\n* column 6: trypsin\nEthanol plate (slot 2)\nAcetonitrile plate (slot 3)", "internal": "5c7384", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/5dcd88/README.json b/protoBuilds/5dcd88/README.json index 5e1ca962f..aac7ed835 100644 --- a/protoBuilds/5dcd88/README.json +++ b/protoBuilds/5dcd88/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol preps a 96 well plate with barcoded, amplified sample. Ultimately, barcoded samples are pooled into a final 1.5mL tube.\nWater and mastermix are added to samples, after which an incubation period follows with subsequent temperature changes. User will load a new PCR plate onto the temperature module for the final sample collecting. User will also pull the sample plate from the deck after the second barcode mastermix is added to barcode samples. After another incubation period with subsequent temperature changes, samples are pooled. The protocol will automatically pause for all steps requiring user intervention.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples for this run\n* P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 Multi-Channel Pipette.\n* Park Tips?: Specify whether or not you would like to park tips for this run\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel\n", + "description": "This protocol preps a 96 well plate with barcoded, amplified sample. Ultimately, barcoded samples are pooled into a final 1.5mL tube.\nWater and mastermix are added to samples, after which an incubation period follows with subsequent temperature changes. User will load a new PCR plate onto the temperature module for the final sample collecting. User will also pull the sample plate from the deck after the second barcode mastermix is added to barcode samples. After another incubation period with subsequent temperature changes, samples are pooled. The protocol will automatically pause for all steps requiring user intervention.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples for this run\n P20 Multi-Channel Mount: Specify which mount (left or right) to host the P20 Multi-Channel Pipette.\n Park Tips?: Specify whether or not you would like to park tips for this run\n P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel\n", "internal": "5dcd88", "labware": "\nNEST 100ul PCR Plate Full Skirt\nOpentrons 20\u00b5L Filter Tips\nOpentrons 200\u00b5L Filter Tips\nNEST 12 Well Reservoir 195mL\nOpentrons 4-in-1 Tube Rack Set\n", "markdown": { diff --git a/protoBuilds/5f37a2/README.json b/protoBuilds/5f37a2/README.json index db5178103..2c19eb3a3 100644 --- a/protoBuilds/5f37a2/README.json +++ b/protoBuilds/5f37a2/README.json @@ -5,7 +5,7 @@ "MagneSil" ] }, - "description": "This protocol performs a nucleic acid purification protocol based on the MagneSil Plasmid Purification System from Promega.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nEppendorf Deep Well Plate 500\u00b5L\nEppendorf Deep Well Plate 2000\u00b5L\nCorning 96-Well Plate, 360\u00b5L\nUSA Scientific 12-Well Reservoir, 22mL\nReagents\nSamples\n\n\n\nSlot 1: Opentrons 50/300\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\nSlot 2: Opentrons 50/300\u00b5L Tips, if needed\nSlot 3: Opentrons 50/300\u00b5L Tips, if needed\nSlot 4: Opentrons 50/300\u00b5L Tips, if needed\nSlot 5: Opentrons 50/300\u00b5L Tips, if needed\nSlot 6: Opentrons 50/300\u00b5L Tips, if needed\nSlot 7: Opentrons 50/300\u00b5L Tips, if needed\nSlot 8: Corning 96-Well Plate\nSlot 9: Eppendorf Deep Well Plate 500\u00b5L, with samples\nSlot 10: Opentrons Magnetic Module with Eppendorf Deep Well Plate 2000\u00b5L\nSlot 11: USA Scientific 12-Well Reservoir\n* A1: Resuspension Buffer\n* A2: Lysis Solution\n* A3: Neutralization Buffer\n* A4: MagneSil Blue\n* A5: MagneSil Red\n* A6: 80% Ethanol Solution\n* A7: Elution Buffer", + "description": "This protocol performs a nucleic acid purification protocol based on the MagneSil Plasmid Purification System from Promega.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips\nEppendorf Deep Well Plate 500\u00b5L\nEppendorf Deep Well Plate 2000\u00b5L\nCorning 96-Well Plate, 360\u00b5L\nUSA Scientific 12-Well Reservoir, 22mL\nReagents\nSamples\n\n\n\nSlot 1: Opentrons 50/300\u00b5L Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\nSlot 2: Opentrons 50/300\u00b5L Tips, if needed\nSlot 3: Opentrons 50/300\u00b5L Tips, if needed\nSlot 4: Opentrons 50/300\u00b5L Tips, if needed\nSlot 5: Opentrons 50/300\u00b5L Tips, if needed\nSlot 6: Opentrons 50/300\u00b5L Tips, if needed\nSlot 7: Opentrons 50/300\u00b5L Tips, if needed\nSlot 8: Corning 96-Well Plate\nSlot 9: Eppendorf Deep Well Plate 500\u00b5L, with samples\nSlot 10: Opentrons Magnetic Module with Eppendorf Deep Well Plate 2000\u00b5L\nSlot 11: USA Scientific 12-Well Reservoir\n A1: Resuspension Buffer\n A2: Lysis Solution\n A3: Neutralization Buffer\n A4: MagneSil Blue\n A5: MagneSil Red\n A6: 80% Ethanol Solution\n* A7: Elution Buffer", "internal": "5fe7a2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/5f791f/README.json b/protoBuilds/5f791f/README.json index b55a4eccf..48cd91887 100644 --- a/protoBuilds/5f791f/README.json +++ b/protoBuilds/5f791f/README.json @@ -29,6 +29,6 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nOpentrons P300 8 Channel Electronic Pipette (GEN2)\nOpentrons P20 8 Channel Electronic Pipette (GEN2)\n\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "Plate on slot 2:\n* green: source samples for PCR prep\nReservoir on slot 4:\n* blue: magnetic beads\n* pink: ethanol\n* purple: elution buffer\n* orange: waste (loaded empty)\n", + "reagent-setup": "Plate on slot 2:\n* green: source samples for PCR prep\nReservoir on slot 4:\n blue: magnetic beads\n pink: ethanol\n purple: elution buffer\n orange: waste (loaded empty)\n", "title": "PCR Prep and Magnetic Bead Cleanup" } \ No newline at end of file diff --git a/protoBuilds/5f7d18/README.json b/protoBuilds/5f7d18/README.json index f83150851..0615cde70 100644 --- a/protoBuilds/5f7d18/README.json +++ b/protoBuilds/5f7d18/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This protocol isolates nucleic acid using a MagBio CTL lysis buffer and MAG-S1 particle beads suspended in 100% isopropanol. 200\u00b5L of sample is pre-loaded into each well within a Kingfisher deep-well plate on the Opentrons magnetic module. The sample undergoes extraction with 2 ethanol washes. The eluate is then transferred to a full-skirted PCR plate along with PCR master-mix for further processing.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nP20 Single Pipette\nP300 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons NEST 96 well plate 100ul PCR full skirt\nOpentrons NEST 12-Well Reservoir\nOpentrons 4-in-1 Tube Rack Set (24-tube insert)\n\n\n\nFor this protocol, be sure that the pipettes (P20 and P300) are attached.\nUsing the customization fields below, set up your protocol.\n* Number of columns: Specify the number of columns of samples loaded onto the NEST deep well plate. Note that runs should only be completed in multiples of full columns (8 samples).\n* Sample and lysis buffer mix repetitions: Specify the number of repetitions to mix the sample and lysis buffer as mentioned in Step 1 of the MAGBIO protocol\n* Mix repetitions before first magnetic engage: Specify the number of mix repetitions to re-suspend the MAG-S1 particles before use (i.e. \"shake well\" in Step 3 of the MAGBIO protocol).\n* Incubation time: Specify the amount of incubation time to allow RNA to bind to the beads\n* Magnetic bead engagement time: Specify the amount of time to engage the magnet for every engagement in protocol\n* Aspiration height from bottom of well (removing supernatant): Specify the height from the bottom of the well in which the pipette will aspirate from when removing supernatant.\n* Multi_channel pipette aspiration flow rate (ul/s): Specify the aspiration flow rate\n* Multi-channel pippette dispense flow rate (ul/s): Specify the dispense flow rate\n* Distance from side of well opposite beads (1mm - 4.15mm): Specify the distance from the side of the well opposite the engaged magnetic beads to aspirate from. A value of 4.15mm returns the center of the well, with 1mm returning 1mm from the side of the well opposite the engaged beads.\n* Bead drying time: Specify the amount of incubation time for the beads to dry at room temperature while magnetically engaged.\n* Bead drying time (with nuclease free water): Specify the amount of time to to dry the beads at room temperature after adding nuclease free water.\n* Nuclease water volume: Specify the amount of nuclease free water to add to the beads\n* P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\n* P300 multi GEN2 mount: Specify which mount to load the P300 multi GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 300ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1: Opentrons Magnetic Module with loaded NEST 96 2mL deep well plate. 200ul of viral sample pre-loaded into each well.\nSlot 2, 5: Opentrons 96 Filter Tip Rack 20 \u00b5L\nSlot 3, 6, 9: Opentrons 96 Filter Tip Rack 200 \u00b5L\nSlot 4: Opentrons NEST 12-Well Reservoir (empty)\nSlot 7: Opentrons 4-in-1 Tube Rack Set. Mastermix loaded into tubes A1, B1.\nSlot 8: Opentrons NEST 96 well plate 100ul PCR full skirt\nSlot 10: Opentrons NEST 12-Well Reservoir with ethanol loaded\nSlot 11: Opentrons NEST 12-Well Reservoir with CTL medium, isopropanol + beads, and nuclease free water loaded\nNote NEST 12-Well Reservoir with Reagents on Slot 11\nThe minimum volume of reagents in the NEST 12-Well Reservoir will be calculated dependent on the number of columns specified and displayed in the Opentrons app prior to beginning the run. \nEthanol is loaded into all 12 wells on the Nest 12-well reservoir on Slot 10.\n\nCTL medium is loaded onto the first two wells, isopropanol + beads onto wells 4-7, and nuclease free water loaded onto well 12 of the Nest 12-Well reservoir on Slot 11.\n", + "description": "This protocol isolates nucleic acid using a MagBio CTL lysis buffer and MAG-S1 particle beads suspended in 100% isopropanol. 200\u00b5L of sample is pre-loaded into each well within a Kingfisher deep-well plate on the Opentrons magnetic module. The sample undergoes extraction with 2 ethanol washes. The eluate is then transferred to a full-skirted PCR plate along with PCR master-mix for further processing.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nP20 Single Pipette\nP300 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons NEST 96 well plate 100ul PCR full skirt\nOpentrons NEST 12-Well Reservoir\nOpentrons 4-in-1 Tube Rack Set (24-tube insert)\n\n\n\nFor this protocol, be sure that the pipettes (P20 and P300) are attached.\nUsing the customization fields below, set up your protocol.\n Number of columns: Specify the number of columns of samples loaded onto the NEST deep well plate. Note that runs should only be completed in multiples of full columns (8 samples).\n Sample and lysis buffer mix repetitions: Specify the number of repetitions to mix the sample and lysis buffer as mentioned in Step 1 of the MAGBIO protocol\n Mix repetitions before first magnetic engage: Specify the number of mix repetitions to re-suspend the MAG-S1 particles before use (i.e. \"shake well\" in Step 3 of the MAGBIO protocol).\n Incubation time: Specify the amount of incubation time to allow RNA to bind to the beads\n Magnetic bead engagement time: Specify the amount of time to engage the magnet for every engagement in protocol\n Aspiration height from bottom of well (removing supernatant): Specify the height from the bottom of the well in which the pipette will aspirate from when removing supernatant.\n Multi_channel pipette aspiration flow rate (ul/s): Specify the aspiration flow rate\n Multi-channel pippette dispense flow rate (ul/s): Specify the dispense flow rate\n Distance from side of well opposite beads (1mm - 4.15mm): Specify the distance from the side of the well opposite the engaged magnetic beads to aspirate from. A value of 4.15mm returns the center of the well, with 1mm returning 1mm from the side of the well opposite the engaged beads.\n Bead drying time: Specify the amount of incubation time for the beads to dry at room temperature while magnetically engaged.\n Bead drying time (with nuclease free water): Specify the amount of time to to dry the beads at room temperature after adding nuclease free water.\n Nuclease water volume: Specify the amount of nuclease free water to add to the beads\n P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\n P300 multi GEN2 mount: Specify which mount to load the P300 multi GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 300ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1: Opentrons Magnetic Module with loaded NEST 96 2mL deep well plate. 200ul of viral sample pre-loaded into each well.\nSlot 2, 5: Opentrons 96 Filter Tip Rack 20 \u00b5L\nSlot 3, 6, 9: Opentrons 96 Filter Tip Rack 200 \u00b5L\nSlot 4: Opentrons NEST 12-Well Reservoir (empty)\nSlot 7: Opentrons 4-in-1 Tube Rack Set. Mastermix loaded into tubes A1, B1.\nSlot 8: Opentrons NEST 96 well plate 100ul PCR full skirt\nSlot 10: Opentrons NEST 12-Well Reservoir with ethanol loaded\nSlot 11: Opentrons NEST 12-Well Reservoir with CTL medium, isopropanol + beads, and nuclease free water loaded\nNote NEST 12-Well Reservoir with Reagents on Slot 11\nThe minimum volume of reagents in the NEST 12-Well Reservoir will be calculated dependent on the number of columns specified and displayed in the Opentrons app prior to beginning the run. \nEthanol is loaded into all 12 wells on the Nest 12-well reservoir on Slot 10.\n\nCTL medium is loaded onto the first two wells, isopropanol + beads onto wells 4-7, and nuclease free water loaded onto well 12 of the Nest 12-Well reservoir on Slot 11.\n", "internal": "5f7d18", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6030b7/README.json b/protoBuilds/6030b7/README.json index c5fc17396..5fd2473c4 100644 --- a/protoBuilds/6030b7/README.json +++ b/protoBuilds/6030b7/README.json @@ -5,7 +5,7 @@ "Lexogen QuantSeq" ] }, - "description": "This protocol performs the Lexogen QuantSeq 3'mRNA FWD NGS library prep for up to 96 samples.\n\n\n\nNEST 0.1mL 96-well PCR plates, full skirt\nOpentrons 4-in-1 tuberack set with 4x6 insert holding NEST 1.5mL microcentrifuge tubes\nOpentrons magnetic module\nOpentrons temperature module with 4x6 aluminum block holding NEST 1.5mL microcentrifuge tubes\nOpentrons P20 GEN2 single-channel electronic pipette\nOpentrons P300 multi-channel electronic pipette\nOpentrons 10/20\u00b5l tipracks\nOpentrons 50/300\u00b5l tipracks\n\n\n\n4x6 tuberack (slot 2):\n* tube A1: RS\n* tube A2: SS1\n* tube A3: SS2\n4x6 aluminum block on temperature module (slot 7):\n* tube A1: FS1\n* tube A2: FS2/E1\n* tube A3: PB\n* tube A4: EB\n* tube A5: PS\n* tube A6: PCR/E3", + "description": "This protocol performs the Lexogen QuantSeq 3'mRNA FWD NGS library prep for up to 96 samples.\n\n\n\nNEST 0.1mL 96-well PCR plates, full skirt\nOpentrons 4-in-1 tuberack set with 4x6 insert holding NEST 1.5mL microcentrifuge tubes\nOpentrons magnetic module\nOpentrons temperature module with 4x6 aluminum block holding NEST 1.5mL microcentrifuge tubes\nOpentrons P20 GEN2 single-channel electronic pipette\nOpentrons P300 multi-channel electronic pipette\nOpentrons 10/20\u00b5l tipracks\nOpentrons 50/300\u00b5l tipracks\n\n\n\n4x6 tuberack (slot 2):\n tube A1: RS\n tube A2: SS1\n* tube A3: SS2\n4x6 aluminum block on temperature module (slot 7):\n tube A1: FS1\n tube A2: FS2/E1\n tube A3: PB\n tube A4: EB\n tube A5: PS\n tube A6: PCR/E3", "internal": "6030b7", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/60d861-2/README.json b/protoBuilds/60d861-2/README.json index b848870f7..456000b4f 100644 --- a/protoBuilds/60d861-2/README.json +++ b/protoBuilds/60d861-2/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "deck-setup": "\n* green: RT Mix\n* blue: sample from part 1\n", + "deck-setup": "\n green: RT Mix\n blue: sample from part 1\n", "description": "Links:\n\n\nPart 1\n\n\nPart 2\n\n\nPart 3\n\n\nThis protocol performs part 2/3 of a custom CYP Induction PCR prep.\n", "internal": "60d861", "labware": "\nThermoFisher MicroAmp\u2122 Fast Optical 96-Well Reaction Plate, 0.1 mL\nNEST 1-Well Reservoirs, 195 mL\nOpentrons 20\u00b5L Tips\n", diff --git a/protoBuilds/60d861-3/README.json b/protoBuilds/60d861-3/README.json index 50318ae13..d7d1c4ab6 100644 --- a/protoBuilds/60d861-3/README.json +++ b/protoBuilds/60d861-3/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "deck-setup": "\n* green: Master Mix\n* blue: sample from part 2\n", + "deck-setup": "\n green: Master Mix\n blue: sample from part 2\n", "description": "Links:\n\n\nPart 1\n\n\nPart 2\n\n\nPart 3\n\n\nThis protocol performs part 3/3 of a custom CYP Induction PCR prep.\n", "internal": "60d861", "labware": "\nThermoFisher MicroAmp\u2122 Fast Optical 96-Well Reaction Plate, 0.1 mL\nNEST 1-Well Reservoirs, 195 mL\nOpentrons 20\u00b5L Tips\n", diff --git a/protoBuilds/60d861/README.json b/protoBuilds/60d861/README.json index 1787e137f..53efb182e 100644 --- a/protoBuilds/60d861/README.json +++ b/protoBuilds/60d861/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "deck-setup": "\n* green: wash buffer\n* blue: waste (empty)\n* pink: elution buffer\n* purple: samples in catcher plate\n", + "deck-setup": "\n green: wash buffer\n blue: waste (empty)\n pink: elution buffer\n purple: samples in catcher plate\n", "description": "Links:\n\n\nPart 1\n\n\nPart 2\n\n\nPart 3\n\n\nThis protocol performs part 1/3 of a custom CYP Induction PCR prep.\n", "internal": "60d861", "labware": "\nLabware name\nNick is working on auto-filling these sections from the protocol (3/28/2021)\n", diff --git a/protoBuilds/657ee9-2/README.json b/protoBuilds/657ee9-2/README.json index c58719b32..bc5494372 100644 --- a/protoBuilds/657ee9-2/README.json +++ b/protoBuilds/657ee9-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 7: Plate containing samples (Destination Plate). Can be on Temperature Module or the Thermocycler Module.\n\nSlot 4: Plate containing FuPa in column 2. Can be on Temperature Module.\n\nSlot 3: Opentrons 20\u00b5L Filter Tip Rack\n", - "description": "This is the second part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Partial Digestion' portion of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA (Columns with Samples).\nExplanation of complex parameters below:\n* Columns with Samples: Specify which columns should we receive the FuPa reagent. Column numbers should be separated by a comma (,).\n* Module for Destination Plate: Select which module you are using for the destination plate (containing samples). If you are not using the Opentrons Thermocycler Module, you will be prompted to remove the plate after liquid handling to an off-deck thermal cycler.\n* Module for Reagent Plate: Select which module you will use for the plate containing mastermix.\n* P20-Multi Mount: Select which mount the P20 Multi-Channel Pipette is attached to. \n", + "description": "This is the second part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Partial Digestion' portion of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA (Columns with Samples).\nExplanation of complex parameters below:\n Columns with Samples: Specify which columns should we receive the FuPa reagent. Column numbers should be separated by a comma (,).\n Module for Destination Plate: Select which module you are using for the destination plate (containing samples). If you are not using the Opentrons Thermocycler Module, you will be prompted to remove the plate after liquid handling to an off-deck thermal cycler.\n Module for Reagent Plate: Select which module you will use for the plate containing mastermix.\n P20-Multi Mount: Select which mount the P20 Multi-Channel Pipette is attached to. \n", "internal": "657ee9", "labware": "\nNEST 96-Well PCR Plates\nOpentrons 20\u00b5L Filter Tip Rack\n", "markdown": { diff --git a/protoBuilds/657ee9-3/README.json b/protoBuilds/657ee9-3/README.json index a8a30b535..d3c68f0da 100644 --- a/protoBuilds/657ee9-3/README.json +++ b/protoBuilds/657ee9-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 7: [Plate]((https://shop.opentrons.com/nest-0-1-ml-96-well-pcr-plate-full-skirt/) containing samples (Destination Plate). Can be on Temperature Module or the Thermocycler Module.\n\nSlot 4: [Plate]((https://shop.opentrons.com/nest-0-1-ml-96-well-pcr-plate-full-skirt/) containing Switch Solution, DNA Ligase, and IonCode Adapters or diluted Ion Xpress barcode adapter mix. Can be on Temperature Module.\n\nSlot 3: Opentrons 20\u00b5L Filter Tip Rack", - "description": "This is the third part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Ligate Adapters' portion of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA (Columns with Samples).\nExplanation of complex parameters below:\n* Columns with Samples: Specify which columns should we receive the FuPa reagent. Column numbers should be separated by a comma (,).\n* Module for Destination Plate: Select which module you are using for the destination plate (containing samples). If you are not using the Opentrons Thermocycler Module, you will be prompted to remove the plate after liquid handling to an off-deck thermal cycler.\n* Module for Reagent Plate: Select which module you will use for the plate containing mastermix.\n* P20-Multi Mount: Select which mount the P20 Multi-Channel Pipette is attached to. \n", + "description": "This is the third part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Ligate Adapters' portion of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA (Columns with Samples).\nExplanation of complex parameters below:\n Columns with Samples: Specify which columns should we receive the FuPa reagent. Column numbers should be separated by a comma (,).\n Module for Destination Plate: Select which module you are using for the destination plate (containing samples). If you are not using the Opentrons Thermocycler Module, you will be prompted to remove the plate after liquid handling to an off-deck thermal cycler.\n Module for Reagent Plate: Select which module you will use for the plate containing mastermix.\n P20-Multi Mount: Select which mount the P20 Multi-Channel Pipette is attached to. \n", "internal": "657ee9-3", "labware": "\nNEST 96-Well PCR Plates\nOpentrons 20\u00b5L Filter Tip Rack\n", "markdown": { @@ -33,7 +33,7 @@ "pipettes": "\nP20 Multi-Channel Pipette\n", "process": "\nInput your protocol parameters above.\nDownload your protocol.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\nFor each column of samples, the P20 Multi-Channel Pipette will pick up a set of tips, transfer 4\u00b5L of Switch Solution from column 3 of the reagent plate to the sample/destination plate, then discard the tips.\nFor each column of samples, the P20 Multi-Channel Pipette will pick up a set of tips, transfer 2\u00b5L of IonCode Adapters or diluted Ion Xpress barcode adapter mix from the corresponding column of the reagent plate to the sample/destination plate, then discard the tips.\nFor each column of samples, the P20 Multi-Channel Pipette will pick up a set of tips, transfer 2\u00b5L of DNA Ligase from column 4 of the reagent plate to the sample/destination plate, mix 5 times, then discard the tips.\nIf using the Thermocycler Module, the thermal cycling steps will be performed on the OT-2. If not, the user will be prompted to move their plate to an off-deck thermal cycler.\n", - "reagent-setup": "[Plate]((https://shop.opentrons.com/nest-0-1-ml-96-well-pcr-plate-full-skirt/) (optional, on Temperature Module) in Slot 4:\n* Column 3: Switch Solution (yellow cap)\n* Column 4: DNA Ligase (blue cap)\n* Column 5+: IonCode Adapters or diluted Ion Xpress barcode adapter mix (should be equal to the number of columns of samples)\n", + "reagent-setup": "Plate in Slot 4:\n Column 3: Switch Solution (yellow cap)\n Column 4: DNA Ligase (blue cap)\n Column 5+: IonCode Adapters or* diluted Ion Xpress barcode adapter mix (should be equal to the number of columns of samples)\n", "reagents": [ "Oncomine Focus Assay" ], diff --git a/protoBuilds/657ee9-4/README.json b/protoBuilds/657ee9-4/README.json index d84329514..78431cf75 100644 --- a/protoBuilds/657ee9-4/README.json +++ b/protoBuilds/657ee9-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 1: [NEST 96-Well PCR Plates containing samples on the Magnetic Module.\n\nSlot 2: NEST 12-Well Reservoir, 15mL containing reagents. \n\nSlot 3: NEST 96-Well PCR Plates, empty for elutes.\n\nSlot 4: Opentrons 200\u00b5L Filter Tip Rack\n\nSlot 5: Opentrons 200\u00b5L Filter Tip Rack\n", - "description": "This is the fourth (and last) part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Purify The Library' and the 'Elute The Library' portions of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA (Columns with Samples).\nUpdate: Protocol was updated to accommodate single column input.\nExplanation of complex parameters below:\n* Columns with Samples: Specify which columns should we receive the FuPa reagent. Column numbers should be separated by a comma (,).\n* P300-Multi Mount: Select which mount the P300 Multi-Channel Pipette is attached to. \n", + "description": "This is the fourth (and last) part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Purify The Library' and the 'Elute The Library' portions of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA (Columns with Samples).\nUpdate: Protocol was updated to accommodate single column input.\nExplanation of complex parameters below:\n Columns with Samples: Specify which columns should we receive the FuPa reagent. Column numbers should be separated by a comma (,).\n P300-Multi Mount: Select which mount the P300 Multi-Channel Pipette is attached to. \n", "internal": "657ee9-4", "labware": "\nNEST 96-Well PCR Plates\nNEST 12-Well Reservoir, 15mL\nOpentrons 200\u00b5L Filter Tip Rack\n", "markdown": { @@ -30,7 +30,7 @@ "pipettes": "\nP300 Multi-Channel Pipette\n", "process": "\nInput your protocol parameters above.\nDownload your protocol.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\nFor each column of samples, the P300 Multi-Channel Pipette will pick up a set of tips, transfer 45\u00b5L of Agencout AMPure XP Reagent from Column 1 of the NEST 12-Well Reservoir to the plate containing samples, mix 5 times, then discard the tips.\nThere will be a 5 minute incubation period (Magnetic Module disengaged).\nThere will be a 2 minute incubation period (Magnetic Module engaged).\nMagnetic Module will disengage.\nFor each column of sample, the P300 Multi-Channel Pipette will pick up a set of tips, transfer 75\u00b5L supernatant to Column 11 of the NEST 12-Well Reservoir, then discard tips.\nFor each column of samples, the P300 Multi-Channel Pipette will pick up a set of tips, transfer 150\u00b5L of Ethanol from Column 3 of the NEST 12-Well Reservoir to the plate containing samples, mix 5 times, then discard the tips.\nThere will be a 2 minute incubation period (Magnetic Module engaged).\nFor each column of sample, the P300 Multi-Channel Pipette will pick up a set of tips, transfer 150\u00b5L supernatant to Column 11 of the NEST 12-Well Reservoir, then discard tips.\nMagnetic Module will disengage.\nSteps 5-9 will repeat (2nd wash).\nThere will be a 2 minute incubation period (Magnetic Module disengaged).\nFor each column of samples, the P300 Multi-Channel Pipette will pick up a set of tips, transfer 50\u00b5L of Low TE from Column 5 of the NEST 12-Well Reservoir to the plate containing samples, mix 5 times, then discard the tips.\nThere will be a 2 minute incubation period (Magnetic Module disengaged).\nThere will be a 2 minute incubation period (Magnetic Module engaged).\nFor each column of sample, the P300 Multi-Channel Pipette will pick up a set of tips, transfer 50\u00b5L supernatant from the column to the next empty column of the empty NEST 96-Well PCR Plates in Slot 3, then discard tips.\n", - "reagent-setup": "NEST 12-Well Reservoir, 15mL in Slot 2:\n* Column 1: Agencout AMPure XP Reagent\n* Column 3: 70% Fresh Ethanol\n* Column 5: Low TE\n* Column 11: Empty (Liquid Waste)\n", + "reagent-setup": "NEST 12-Well Reservoir, 15mL in Slot 2:\n Column 1: Agencout AMPure XP Reagent\n Column 3: 70% Fresh Ethanol\n Column 5: Low TE\n Column 11: Empty (Liquid Waste)\n", "reagents": [ "Oncomine Focus Assay" ], diff --git a/protoBuilds/657ee9/README.json b/protoBuilds/657ee9/README.json index 79c714069..bfde52463 100644 --- a/protoBuilds/657ee9/README.json +++ b/protoBuilds/657ee9/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slot 7: Plate containing samples (Destination Plate). Can be on Temperature Module or the Thermocycler Module.\n\nSlot 4: Plate containing master mix in column 1. Can be on Temperature Module.\n\nSlot 3: Opentrons 20\u00b5L Filter Tip Rack\n", - "description": "This is the first part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Target Amplification' portion of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples.\n* Master Mix Transfer Volume: Select the volume of mastermix to transfer to the samples. 10\u00b5L is for cDNA synthesis and the other options are for DNA.\n* Module for Destination Plate: Select which module you are using for the destination plate (containing samples). If you are not using the Opentrons Thermocycler Module, you will be prompted to remove the plate after liquid handling to an off-deck thermal cycler.\n* Number of Cycles: If using the Opentrons Thermocycler Module, you can specify the number of cycles. For more information, please see the manual.\n* Module for Reagent Plate: Select which module you will use for the plate containing mastermix.\n* P20-Multi Mount: Select which mount the P20 Multi-Channel Pipette is attached to. \n", + "description": "This is the first part in a multi-part protocol designed to automate the Oncomine Focus Assay. For a detailed description of the manual protocol, please see this resource.\nIn this protocol, the OT-2 automates the 'Target Amplification' portion of the protocol. Using the complex parameters described below, the user can specify which, if any, modules they are using and select from different options pertaining to RNA/cDNA and DNA.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples.\n Master Mix Transfer Volume: Select the volume of mastermix to transfer to the samples. 10\u00b5L is for cDNA synthesis and the other options are for DNA.\n Module for Destination Plate: Select which module you are using for the destination plate (containing samples). If you are not using the Opentrons Thermocycler Module, you will be prompted to remove the plate after liquid handling to an off-deck thermal cycler.\n Number of Cycles: If using the Opentrons Thermocycler Module, you can specify the number of cycles. For more information, please see the manual.\n Module for Reagent Plate: Select which module you will use for the plate containing mastermix.\n P20-Multi Mount: Select which mount the P20 Multi-Channel Pipette is attached to. \n", "internal": "657ee9", "labware": "\nNEST 96-Well PCR Plates\nOpentrons 20\u00b5L Filter Tip Rack\n", "markdown": { diff --git a/protoBuilds/659888/README.json b/protoBuilds/659888/README.json index cc3626186..f5ba03cb0 100644 --- a/protoBuilds/659888/README.json +++ b/protoBuilds/659888/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol dispenses diluted phage by column in a source 360ul corning plate to all specified agar plates. The tips are to not touch the agar medium but instead dispense right above it, saving up to 5 times the number of tips per run. Column 1 of the source plate is dispensed into into column 1 of all agar plates in a multi-dispense fashion to additionally save time.\nExplanation of complex parameters below:\n* Number of plates: Specify the number of agar plates (1-5) to fill for this run.\n* Number of columns in each plate: Specify the number of columns (1-12) in each agar plate to fill.\n* Number of rows in each plate: Specify the number of rows (1-8) in each agar plate to fill.\n* P20 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n", + "description": "This protocol dispenses diluted phage by column in a source 360ul corning plate to all specified agar plates. The tips are to not touch the agar medium but instead dispense right above it, saving up to 5 times the number of tips per run. Column 1 of the source plate is dispensed into into column 1 of all agar plates in a multi-dispense fashion to additionally save time.\nExplanation of complex parameters below:\n Number of plates: Specify the number of agar plates (1-5) to fill for this run.\n Number of columns in each plate: Specify the number of columns (1-12) in each agar plate to fill.\n Number of rows in each plate: Specify the number of rows (1-8) in each agar plate to fill.\n P20 Multi-Channel Pipette Mount: Specify which mount (left or right) to host the P20 multi-channel pipette.\n", "internal": "659888", "labware": "\nCorning 96 Well Plate 360 \u00b5L Flat\nOpentrons 20uL Filter Tips\nCustom Agar Plates\n", "markdown": { diff --git a/protoBuilds/65ed01/README.json b/protoBuilds/65ed01/README.json index 74380968c..35bfed495 100644 --- a/protoBuilds/65ed01/README.json +++ b/protoBuilds/65ed01/README.json @@ -5,7 +5,7 @@ "Nucleic Acid Purification" ] }, - "description": "This protocol performs a nucleic acid purification with the Opentrons magnetic module.\nLysis buffer is added to sample and mixed. The subsequent lysate is then added to magnetic beads with isopropanol. After mixing, the Opentrons magnetic module is engaged and supernatant is removed and returned to reservoir. Two washes are then performed using wash and elution buffer, respectively. The final elute is transferred to an Opentrons 96-Well Aluminum Block plate. \n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 200\u00b5L Tips\nOpentrons Magnetic Module\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\nNEST 1 Well Reservoir 195 mL\nYDP 96-Well Square Well-Plate 2200ul\n\n\n\nSlot 1: Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\nSlot 2: Opentrons 96 Filter Tip Rack 200 \u00b5L\nSlot 3: Opentrons 96 Filter Tip Rack 200 \u00b5L\nSlot 6: YDP 96-Well Square Well-Plate 2200ul with Magnetic Module\nSlot 11: NEST 1 Well Reservoir 195 mL\n\n\nUsing the customizations field (below), set up your protocol.\n* Distance From Side of well: Specify the distance from the well wall the pipette will aspirate from. The pipette will aspirate from this distance on the well wall opposite that of the magnetic beads. An input value of 4.05 returns the center of the well.\n* Number of Plates: Specify the mount side for the P300 Multi Channel Pipette.", + "description": "This protocol performs a nucleic acid purification with the Opentrons magnetic module.\nLysis buffer is added to sample and mixed. The subsequent lysate is then added to magnetic beads with isopropanol. After mixing, the Opentrons magnetic module is engaged and supernatant is removed and returned to reservoir. Two washes are then performed using wash and elution buffer, respectively. The final elute is transferred to an Opentrons 96-Well Aluminum Block plate. \n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 200\u00b5L Tips\nOpentrons Magnetic Module\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\nNEST 1 Well Reservoir 195 mL\nYDP 96-Well Square Well-Plate 2200ul\n\n\n\nSlot 1: Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\nSlot 2: Opentrons 96 Filter Tip Rack 200 \u00b5L\nSlot 3: Opentrons 96 Filter Tip Rack 200 \u00b5L\nSlot 6: YDP 96-Well Square Well-Plate 2200ul with Magnetic Module\nSlot 11: NEST 1 Well Reservoir 195 mL\n\n\nUsing the customizations field (below), set up your protocol.\n Distance From Side of well: Specify the distance from the well wall the pipette will aspirate from. The pipette will aspirate from this distance on the well wall opposite that of the magnetic beads. An input value of 4.05 returns the center of the well.\n Number of Plates: Specify the mount side for the P300 Multi Channel Pipette.", "internal": "65ed01", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/66aa48/README.json b/protoBuilds/66aa48/README.json index 5eaf8a927..19323b856 100644 --- a/protoBuilds/66aa48/README.json +++ b/protoBuilds/66aa48/README.json @@ -5,7 +5,7 @@ "Cherrypicking" ] }, - "description": "This protocol allows the robot to create up to 4 different pooling samples by consolidating cherrypicked wells from a 96 tall-well plates. The user will need upload one CSV each for increase, no change, decrease, and inactive property changes. Each CSV will contain information of the wells from which to be picked. See Additional Notes for the format of the CSVs, as well as the arrangement of pooling tubes in the Opentrons 4x6 2ml Eppendorf tuberack. If you would like to skip a pool as specified by 1 of the 4 CSV files, upload an empty CSV file corresponding to that pool.\nYour CSV files should contain source wells of the 96-well source plate each on its own line, as in the following:\nA2\nA3\nA4\nA7\nA8\nB3\nB5\nThe pooling tubes are seated in the Opentrons tube rack according to the following setup:\n* inactive: tube A1\n* decrease: tube B1\n* no change: tube C1\n* increase: tube D1", + "description": "This protocol allows the robot to create up to 4 different pooling samples by consolidating cherrypicked wells from a 96 tall-well plates. The user will need upload one CSV each for increase, no change, decrease, and inactive property changes. Each CSV will contain information of the wells from which to be picked. See Additional Notes for the format of the CSVs, as well as the arrangement of pooling tubes in the Opentrons 4x6 2ml Eppendorf tuberack. If you would like to skip a pool as specified by 1 of the 4 CSV files, upload an empty CSV file corresponding to that pool.\nYour CSV files should contain source wells of the 96-well source plate each on its own line, as in the following:\nA2\nA3\nA4\nA7\nA8\nB3\nB5\nThe pooling tubes are seated in the Opentrons tube rack according to the following setup:\n inactive: tube A1\n decrease: tube B1\n no change: tube C1\n increase: tube D1", "internal": "66aa48", "labware": "\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Eppendorf 2 mL Safe-Lock Snapcap\n", "markdown": { diff --git a/protoBuilds/66e60f/README.json b/protoBuilds/66e60f/README.json index 07caa0df2..52b99b6ab 100644 --- a/protoBuilds/66e60f/README.json +++ b/protoBuilds/66e60f/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Slots:\n1. 20 \u00b5L filter tip-rack (B)\n2. Empty\n3. 20 \u00b5L filter tip-rack (A)\n4. Final Plate B\n5. Tuberack\n6. Final Plate A\n7. DNA Plate B\n8. Empty\n9. DNA Plate A\n10. 200 \u00b5L filter tip-rack\n11. Water reservoir\n", - "description": "This protocol performs a custom sample normalization from one or two source plate(s) to one or two final plate(s), diluting with water from a 12 well reservoir on slot 11 based on an input csv file. After normalization the protocol samples 5 \u00b5L from each well from the final plate(s) and dispenses it into a DNA pool tube on the tuberack on slot 5 (the tube in position A2). Sample and diluent volumes are specified via the .csv file in the following format, including the header line (empty lines ignored, also note that this is just an example and that any number of lines less than and up to 2x96 may be specified):\nPlate, Well, SampleID, Concentration, VolumeToDispense\nA, A1, Sample1, 3.28, 12.52,\n...\nA, H12, Sample96, 5.30, 9.70,\nB, A1, Sample97, 6.34, 8.60,\n...\nB, H12, Sample192, 7.34, 5.60,\nThe plate is either A (to Final plate slot 6 from DNA plate slot 9) or B (to Final plate slot 4 from DNA plate slot 7)\nUpdate (Jan 28, 2022): This protocol has been updated. The user can now select between the Opentrons P300 GEN2 Single-Channel pipette or the Opentrons P300 GEN2 8-Channel pipette.\nParameters:\n* .csv input file: Input file (see above)\n* Source plate type: Opentrons compatible 96 well plate containing DNA samples\n* Destination plate type: Opentrons compatible 96 well plates where DNA samples are diluted with water\n* Tuberack/tubes: Tuberack/tube combination for DNA and water bins and DNA pool.\n* P300 type: Single or multichannel: Only used for the initial water distribution\n* Air gap volume: Volume of air for all air gaps, default is 10 \u00b5L\n\n", + "description": "This protocol performs a custom sample normalization from one or two source plate(s) to one or two final plate(s), diluting with water from a 12 well reservoir on slot 11 based on an input csv file. After normalization the protocol samples 5 \u00b5L from each well from the final plate(s) and dispenses it into a DNA pool tube on the tuberack on slot 5 (the tube in position A2). Sample and diluent volumes are specified via the .csv file in the following format, including the header line (empty lines ignored, also note that this is just an example and that any number of lines less than and up to 2x96 may be specified):\nPlate, Well, SampleID, Concentration, VolumeToDispense\nA, A1, Sample1, 3.28, 12.52,\n...\nA, H12, Sample96, 5.30, 9.70,\nB, A1, Sample97, 6.34, 8.60,\n...\nB, H12, Sample192, 7.34, 5.60,\nThe plate is either A (to Final plate slot 6 from DNA plate slot 9) or B (to Final plate slot 4 from DNA plate slot 7)\nUpdate (Jan 28, 2022): This protocol has been updated. The user can now select between the Opentrons P300 GEN2 Single-Channel pipette or the Opentrons P300 GEN2 8-Channel pipette.\nParameters:\n .csv input file: Input file (see above)\n Source plate type: Opentrons compatible 96 well plate containing DNA samples\n Destination plate type: Opentrons compatible 96 well plates where DNA samples are diluted with water\n Tuberack/tubes: Tuberack/tube combination for DNA and water bins and DNA pool.\n P300 type: Single or multichannel: Only used for the initial water distribution\n Air gap volume: Volume of air for all air gaps, default is 10 \u00b5L\n\n", "internal": "66e60f", "labware": "\nNEST 12-Well Reservoirs, 15 mL\nAn Opentrons compatible 96-well sample source plates\nAn Opentrons compatible 96-well target plates\n", "markdown": { diff --git a/protoBuilds/69486f/README.json b/protoBuilds/69486f/README.json index dbe94c73e..d72f4a4a8 100644 --- a/protoBuilds/69486f/README.json +++ b/protoBuilds/69486f/README.json @@ -5,7 +5,7 @@ "KAPA HiFi" ] }, - "deck-setup": "Note that these deck states depict a combination of the maximum number of PCR 1 forward primers.\nStarting state (showing normalization for <= 28 sample + subsample product):\n\n* green on slot 1: starting samples according to above example .csv\n* clear on slot 7 (tubes A1-D2): empty tubes for PCR 1 mix creation\n* orange on slot 7 (A3-D4): unique PCR 1 forward primers (in column order)\n* clear on slot 7 (tubes A5-D6): empty tubes for PCR 2 mix creation\n* blue on slot 8 (A1): water\n* pink on slot 8 (B1): PCR mastermix\n* purple on slot 8 (C1): PCR 1 reverse primer\n* purple on slot 8 (D1): PCR 2 reverse primer\n* dark blue on slot 8 (A2-D3): tubes for normalized pools\n* orange on slot 8 (A4-D5): unique PCR 1 forward primers (in column order)\n* light blue on slot 8 (A6): normalization binding buffer\n* light purple on slot 8 (B6-C6): normalization wash buffer\n* green on slot 8 (D6): normalization elution buffer\nStarting state (showing normalization for <= 28 sample + subsample product):\n\n* green on slot 1: starting samples according to above example .csv\n* clear on slot 7 (tubes A1-D2): empty tubes for PCR 1 mix creation\n* orange on slot 7 (A3-D4): unique PCR 1 forward primers (in column order)\n* clear on slot 7 (tubes A5-D6): empty tubes for PCR 2 mix creation\n* blue on slot 8 (A1): water\n* pink on slot 8 (B1): PCR mastermix\n* purple on slot 8 (C1): PCR 1 reverse primer\n* purple on slot 8 (D1): PCR 2 reverse primer\n* dark blue on slot 8 (A2-D3): tubes for normalized pools\n* orange on slot 8 (A4-D5): unique PCR 1 forward primers (in column order)\n* light blue on slot 11 (A1): normalization binding buffer\n* light purple on slot 11 (A2): normalization wash buffer\n* green on slot 11 (A3): normalization elution buffer\n", + "deck-setup": "Note that these deck states depict a combination of the maximum number of PCR 1 forward primers.\nStarting state (showing normalization for <= 28 sample + subsample product):\n\n green on slot 1: starting samples according to above example .csv\n clear on slot 7 (tubes A1-D2): empty tubes for PCR 1 mix creation\n orange on slot 7 (A3-D4): unique PCR 1 forward primers (in column order)\n clear on slot 7 (tubes A5-D6): empty tubes for PCR 2 mix creation\n blue on slot 8 (A1): water\n pink on slot 8 (B1): PCR mastermix\n purple on slot 8 (C1): PCR 1 reverse primer\n purple on slot 8 (D1): PCR 2 reverse primer\n dark blue on slot 8 (A2-D3): tubes for normalized pools\n orange on slot 8 (A4-D5): unique PCR 1 forward primers (in column order)\n light blue on slot 8 (A6): normalization binding buffer\n light purple on slot 8 (B6-C6): normalization wash buffer\n* green on slot 8 (D6): normalization elution buffer\nStarting state (showing normalization for <= 28 sample + subsample product):\n\n green on slot 1: starting samples according to above example .csv\n clear on slot 7 (tubes A1-D2): empty tubes for PCR 1 mix creation\n orange on slot 7 (A3-D4): unique PCR 1 forward primers (in column order)\n clear on slot 7 (tubes A5-D6): empty tubes for PCR 2 mix creation\n blue on slot 8 (A1): water\n pink on slot 8 (B1): PCR mastermix\n purple on slot 8 (C1): PCR 1 reverse primer\n purple on slot 8 (D1): PCR 2 reverse primer\n dark blue on slot 8 (A2-D3): tubes for normalized pools\n orange on slot 8 (A4-D5): unique PCR 1 forward primers (in column order)\n light blue on slot 11 (A1): normalization binding buffer\n light purple on slot 11 (A2): normalization wash buffer\n* green on slot 11 (A3): normalization elution buffer\n", "description": "This custom protocol performs part 2 of the KAPA HiFi NGS Library Prep kit. The protocol can accommodate up to 8 samples. The operator is prompted to perform PCR and normalization off-deck.\nThe number of samples and subsamples should be specified in a .csv file formatted as follows:\nsample index,# subsamples\n1,1\n2,2\nYou can also access a template file here.\n", "internal": "69486f", "labware": "\nAgilent AriaMx 96 Well PCR Plates 200ul #401490\nOpentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap Tubes\nOpentrons 20\u00b5L Filter Tips\nOpentrons 200\u00b5L Filter Tips\n", diff --git a/protoBuilds/698b9e-part2/README.json b/protoBuilds/698b9e-part2/README.json index 0babe4b3d..8aa7009c7 100644 --- a/protoBuilds/698b9e-part2/README.json +++ b/protoBuilds/698b9e-part2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol is part two of a two part series for performing a custom PCR prep with 1.5 mL Falcon conical tubes. Find Part 1 of the protocol here:\n\nPCR Prep with 1.5 mL Tubes Part 1 - Plate Filling\n\nThis protocol makes a saliva and buffer solution, and then transfers this solution to a mastermix plate for further processing. \nExplanation of complex parameters below:\n* Number of Samples: Specify the number of sample tubes you will use over this run. After samples from all tubes in the tube rack have been moved to the buffer plate, the protocol will pause and ask for the user to replace the tubes. For example, a value of 32 for Number of Samples would ask the user to replace the tube rack once (after 15 samples), and the OT-2 will then only aspirate from the first two tubes after replacement.\n* Aspirate Saliva Delay Time (in seconds): Select the amount of time to delay after aspirating saliva or saliva/buffer solution to allow for full achievement of aspiration.\n* P300 Multi Channel Mount: Specify which side (left or right) to mount the P300 Multi Channel Pipette.\n* P20 Single Channel Mount: Specify which side (left or right) to mount the P20 Single Channel Pipette. \n", + "description": "This protocol is part two of a two part series for performing a custom PCR prep with 1.5 mL Falcon conical tubes. Find Part 1 of the protocol here:\n\nPCR Prep with 1.5 mL Tubes Part 1 - Plate Filling\n\nThis protocol makes a saliva and buffer solution, and then transfers this solution to a mastermix plate for further processing. \nExplanation of complex parameters below:\n Number of Samples: Specify the number of sample tubes you will use over this run. After samples from all tubes in the tube rack have been moved to the buffer plate, the protocol will pause and ask for the user to replace the tubes. For example, a value of 32 for Number of Samples would ask the user to replace the tube rack once (after 15 samples), and the OT-2 will then only aspirate from the first two tubes after replacement.\n Aspirate Saliva Delay Time (in seconds): Select the amount of time to delay after aspirating saliva or saliva/buffer solution to allow for full achievement of aspiration.\n P300 Multi Channel Mount: Specify which side (left or right) to mount the P300 Multi Channel Pipette.\n P20 Single Channel Mount: Specify which side (left or right) to mount the P20 Single Channel Pipette. \n", "internal": "698b9e-part2", "labware": "\nOpentrons Filter Tip Racks 20ul\nOpentrons Filter Tip Racks 200ul\nNunc\u2122 96-Well Polypropylene Storage Microplates\nMicroAmp\u2122 Fast Optical 96-Well Reaction Plate with Barcode, 0.1 mL\nNEST 12-Well Reservoir, 15 mL\n", "markdown": { diff --git a/protoBuilds/698b9e/README.json b/protoBuilds/698b9e/README.json index 4356d355a..451a90e4f 100644 --- a/protoBuilds/698b9e/README.json +++ b/protoBuilds/698b9e/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck setup if running 9 plates. If selecting less than 9 plates, fill the deck slots in numerical order starting from Deck Slot 3.\n\n", - "description": "This protocol is part one of a two part series for performing a custom PCR prep with 1.5 mL Falcon conical tubes. Find Part 2 of the protocol here:\n\nPCR Prep with 1.5 mL Tubes Part 2 - Adding Sample\n\nThis protocol fills one of two plates with either reaction buffer or mastermix as specified by the user. The user can also specify how many plates they would like to fill with buffer, or mastermix. Plates should then be kept in cold storage, ready for use as saliva samples come in.\nExplanation of complex parameters below:\n* Number of Plates: Specify the number of plates you want to populate with reagent.\n* Reagent: Specify whether you would like to fill the number of plates selected above with mastermix, or buffer. 80ul will be transferred if Buffer is selected, while 7.6ul will be transferred to each well in every plate if Mastermix is selected. The P300 Multi Channel pipette is used for Buffer, while the P20 Single Channel Pipette is used for Mastermix.\n* P300 Multi Channel Mount: Specify which side (left or right) to mount the P300 Multi Channel Pipette.\n* P20 Single Channel Mount: Specify which side (left or right) to mount the P20 Single Channel Pipette. \n", + "description": "This protocol is part one of a two part series for performing a custom PCR prep with 1.5 mL Falcon conical tubes. Find Part 2 of the protocol here:\n\nPCR Prep with 1.5 mL Tubes Part 2 - Adding Sample\n\nThis protocol fills one of two plates with either reaction buffer or mastermix as specified by the user. The user can also specify how many plates they would like to fill with buffer, or mastermix. Plates should then be kept in cold storage, ready for use as saliva samples come in.\nExplanation of complex parameters below:\n Number of Plates: Specify the number of plates you want to populate with reagent.\n Reagent: Specify whether you would like to fill the number of plates selected above with mastermix, or buffer. 80ul will be transferred if Buffer is selected, while 7.6ul will be transferred to each well in every plate if Mastermix is selected. The P300 Multi Channel pipette is used for Buffer, while the P20 Single Channel Pipette is used for Mastermix.\n P300 Multi Channel Mount: Specify which side (left or right) to mount the P300 Multi Channel Pipette.\n P20 Single Channel Mount: Specify which side (left or right) to mount the P20 Single Channel Pipette. \n", "internal": "698b9e", "labware": "\nOpentrons Filter Tip Racks 20ul\nOpentrons Filter Tip Racks 200ul\nNunc\u2122 96-Well Polypropylene Storage Microplates\nMicroAmp\u2122 Fast Optical 96-Well Reaction Plate with Barcode, 0.1 mL\n", "markdown": { diff --git a/protoBuilds/69cf81-2/README.json b/protoBuilds/69cf81-2/README.json index b9648215f..1f0256baf 100644 --- a/protoBuilds/69cf81-2/README.json +++ b/protoBuilds/69cf81-2/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "deck-setup": "The following example shows a setup for 16 samples and 6 primers. Note that samples can continue across the plate, and primers can continue down and then across the tuberack.\n* green in reagent reservoir: unique primer, BigDye + water mix\n* blue in sample plate: PCR templates\n\n", + "deck-setup": "The following example shows a setup for 16 samples and 6 primers. Note that samples can continue across the plate, and primers can continue down and then across the tuberack.\n green in reagent reservoir: unique primer, BigDye + water mix\n blue in sample plate: PCR templates\n\n", "description": "This protocol performs a custom PCR prep by transferring samples, primers, BigDye, and water to a clean PCR plate. New tips are used for each transfer, both to avoid contamination and to accurately dispense small volumes (1-6\u00b5l). See below for deck and reagent setups.\nNote that the product of the number of samples multiplied by the number of primers cannot exceed 96, or an exception will be thrown.\nAn example of the transfer scheme is shown in the following schematic:\n\n", "internal": "69cf81", "labware": "\nThermoFisher MicroAmp\u2122 Optical 96-Well Reaction Plate with Barcode #4306737\nNEST 15 Reservoir 12ml\nOpentrons 20\u00b5l Tipracks or Rainin 20\u00b5l Tipracks\n", diff --git a/protoBuilds/69cf81/README.json b/protoBuilds/69cf81/README.json index bab1b6032..7f6af1666 100644 --- a/protoBuilds/69cf81/README.json +++ b/protoBuilds/69cf81/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "deck-setup": "The following example shows a setup for 8 samples and 2 primers. Note that samples can continue across the plate, and primers can continue down and then across the tuberack.\n* green in reagent reservoir: BigDye + water mix\n* pink in primer rack: primer 1\n* orange in primer rack: primer 2\n\n", + "deck-setup": "The following example shows a setup for 8 samples and 2 primers. Note that samples can continue across the plate, and primers can continue down and then across the tuberack.\n green in reagent reservoir: BigDye + water mix\n pink in primer rack: primer 1\n* orange in primer rack: primer 2\n\n", "description": "This protocol performs a custom PCR prep by transferring samples, primers, BigDye, and water to a clean PCR plate. New tips are used for each transfer, both to avoid contamination and to accurately dispense small volumes (1-6\u00b5l). See below for deck and reagent setups.\nNote that the product of the number of samples multiplied by the number of primers cannot exceed 96, or an exception will be thrown.\nAn example of the transfer scheme is shown in the following schematic:\n\n", "internal": "69cf81", "labware": "\nThermoFisher MicroAmp\u2122 Optical 96-Well Reaction Plate with Barcode #4306737\nNEST 15 Reservoir 12ml\nOpentrons 24 Tube Rack with NEST 1.5 mL Snapcap (or equivalent)\nOpentrons 20\u00b5l Tipracks or Rainin 20\u00b5l Tipracks\n", diff --git a/protoBuilds/69db93/README.json b/protoBuilds/69db93/README.json index d85d06484..1f995db02 100644 --- a/protoBuilds/69db93/README.json +++ b/protoBuilds/69db93/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This protocol isolates nucleic acid preloaded onto a NEST 96 deep well plate premixed with magnetic beads. The sample undergoes extraction with one wash step. The eluate is then transferred to a full-skirted PCR plate for further processing. Tips are parked throughout the protocol for potential reuse. No tips are discarded in the trash.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nP300 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons NEST 96 well plate 100ul PCR full skirt\nOpentrons NEST 96 deep well plate 2mL\nOpentrons NEST 12-Well Reservoir\nOpentrons NEST 1-Well Reservoir\n\n\n\nFor this protocol, be sure that the P300 pipette is attached.\nUsing the customization fields below, set up your protocol.\n* Number of samples: Specify the number of samples loaded onto the NEST deep well plate. Note that runs should only be completed in multiples of full columns (8 samples).\n* Aspiration height from bottom of well (removing supernatant): Specify the height from the bottom of the well in which the pipette will aspirate from when removing supernatant.\n* Multi_channel pipette aspiration flow rate for mixing (ul/s): Specify the aspiration flow rate for all mix steps.\n* Multi_channel pipette dispense flow rate for mixing (ul/s): Specify the dispense flow rate for all mix steps.\n* Distance from side of well opposite beads (1mm - 4.15mm): Specify the distance from the side of the well opposite the engaged magnetic beads to aspirate from. A value of 4.15mm returns the center of the well, with 1mm returning 1mm from the side of the well opposite the engaged beads.\n* P300 multi GEN2 mount: Specify which mount to load the P300 multi GEN2 pipette.\nNote About Reagents\nBind buffer + Etoh, wash buffer, and TE in the Nest 12 well reservoir should be loaded into their respective wells prior to the protocol. The minimum volume of which (dependent on how many samples are being run) can be found below.\n\n\n\nLabware Setup\nSlots 1: Opentrons Magnetic Module with loaded NEST 96 2mL deep well plate. 400ul sample and pre-mix loaded in each well.\nSlot 2: Nest 12 well reservoir with binding buffer + Etoh, wash buffer, and TE loaded.\nSlot 3: Opentrons NEST 96 well plate 100ul PCR full skirt.\nSlot 4, 7, 10: Opentrons 96 Filter Tip Rack 200 \u00b5L (empty for parking).\nSlot 5, 6, 8, 9: Opentrons 96 Filter Tip Rack 200 \u00b5L.\nSlot 11: Nest 1-well reservoir", + "description": "This protocol isolates nucleic acid preloaded onto a NEST 96 deep well plate premixed with magnetic beads. The sample undergoes extraction with one wash step. The eluate is then transferred to a full-skirted PCR plate for further processing. Tips are parked throughout the protocol for potential reuse. No tips are discarded in the trash.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nP300 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons NEST 96 well plate 100ul PCR full skirt\nOpentrons NEST 96 deep well plate 2mL\nOpentrons NEST 12-Well Reservoir\nOpentrons NEST 1-Well Reservoir\n\n\n\nFor this protocol, be sure that the P300 pipette is attached.\nUsing the customization fields below, set up your protocol.\n Number of samples: Specify the number of samples loaded onto the NEST deep well plate. Note that runs should only be completed in multiples of full columns (8 samples).\n Aspiration height from bottom of well (removing supernatant): Specify the height from the bottom of the well in which the pipette will aspirate from when removing supernatant.\n Multi_channel pipette aspiration flow rate for mixing (ul/s): Specify the aspiration flow rate for all mix steps.\n Multi_channel pipette dispense flow rate for mixing (ul/s): Specify the dispense flow rate for all mix steps.\n Distance from side of well opposite beads (1mm - 4.15mm): Specify the distance from the side of the well opposite the engaged magnetic beads to aspirate from. A value of 4.15mm returns the center of the well, with 1mm returning 1mm from the side of the well opposite the engaged beads.\n P300 multi GEN2 mount: Specify which mount to load the P300 multi GEN2 pipette.\nNote About Reagents\nBind buffer + Etoh, wash buffer, and TE in the Nest 12 well reservoir should be loaded into their respective wells prior to the protocol. The minimum volume of which (dependent on how many samples are being run) can be found below.\n\n\n\nLabware Setup\nSlots 1: Opentrons Magnetic Module with loaded NEST 96 2mL deep well plate. 400ul sample and pre-mix loaded in each well.\nSlot 2: Nest 12 well reservoir with binding buffer + Etoh, wash buffer, and TE loaded.\nSlot 3: Opentrons NEST 96 well plate 100ul PCR full skirt.\nSlot 4, 7, 10: Opentrons 96 Filter Tip Rack 200 \u00b5L (empty for parking).\nSlot 5, 6, 8, 9: Opentrons 96 Filter Tip Rack 200 \u00b5L.\nSlot 11: Nest 1-well reservoir", "internal": "69db93", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6a93a2-part2/README.json b/protoBuilds/6a93a2-part2/README.json index 91939a90a..c032e17c4 100644 --- a/protoBuilds/6a93a2-part2/README.json +++ b/protoBuilds/6a93a2-part2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol is part two of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n* Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n* Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n* Swift Rapid NGS Part 4 - SPRI Clean\n* Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart two of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nMake Adaptase Mastermix\nRun Thermocycler Profile\nAdd Adaptase Mastermix\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples that will be processed.\n* Adaptase Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n* Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n* P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", + "description": "This protocol is part two of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n Swift Rapid NGS Part 4 - SPRI Clean\n Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart two of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nMake Adaptase Mastermix\nRun Thermocycler Profile\nAdd Adaptase Mastermix\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples that will be processed.\n Adaptase Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", "internal": "6a93a2-part2", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 20\u00b5L Tips\nOpentrons 200uL Tips\nOpentrons 24-Tube Aluminum Block\n", "markdown": { diff --git a/protoBuilds/6a93a2-part3/README.json b/protoBuilds/6a93a2-part3/README.json index 2b309e7c2..2b1928f5c 100644 --- a/protoBuilds/6a93a2-part3/README.json +++ b/protoBuilds/6a93a2-part3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol is part three of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n* Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n* Swift Rapid NGS Part 2 - Adaptase\n* Swift Rapid NGS Part 4 - SPRI Clean\n* Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart three of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nExtension\nExtraction\nLigation\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples that will be processed.\n* PCR Mastermix and Ligation Mastermix Overage Percent (0-10%): Specify the percent overage of PCR and Ligation Mastermix to make and ultimately add to samples.\n* Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n* Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n* P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", + "description": "This protocol is part three of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n Swift Rapid NGS Part 2 - Adaptase\n Swift Rapid NGS Part 4 - SPRI Clean\n Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart three of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nExtension\nExtraction\nLigation\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples that will be processed.\n PCR Mastermix and Ligation Mastermix Overage Percent (0-10%): Specify the percent overage of PCR and Ligation Mastermix to make and ultimately add to samples.\n Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", "internal": "6a93a2", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 20\u00b5L Tips\nOpentrons 200uL Tips\nOpentrons 24-Tube Aluminum Block\n", "markdown": { diff --git a/protoBuilds/6a93a2-part4/README.json b/protoBuilds/6a93a2-part4/README.json index b9579f331..ee49f930d 100644 --- a/protoBuilds/6a93a2-part4/README.json +++ b/protoBuilds/6a93a2-part4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol is part four of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n* Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n* Swift Rapid NGS Part 2 - Adaptase\n* Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n* Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart four of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nSPRI Cleanup\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples that will be processed.\n* Reverse Transcription Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n* Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n* Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n* P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", + "description": "This protocol is part four of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n Swift Rapid NGS Part 2 - Adaptase\n Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart four of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nSPRI Cleanup\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples that will be processed.\n Reverse Transcription Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", "internal": "6a93a2-part4", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 20\u00b5L Tips\nOpentrons 200uL Tips\nOpentrons 24-Tube Aluminum Block\n", "markdown": { diff --git a/protoBuilds/6a93a2-part5/README.json b/protoBuilds/6a93a2-part5/README.json index d1e4c99ad..f047416db 100644 --- a/protoBuilds/6a93a2-part5/README.json +++ b/protoBuilds/6a93a2-part5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol is part five of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n* Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n* Swift Rapid NGS Part 2 - Adaptase\n* Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n* Swift Rapid NGS Part 4 - SPRI Clean\nPart five of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nIndexing PCR\nSPRI Cleanup\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples that will be processed.\n* PCR Mastermix Overage Percent: Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n* Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n* Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n* Index Start Column: Specify which column on the index plate to begin aspirating from.\n* Number of Thermocycler Cycles: Specify the number of repetitions samples will undergo a (20 second, 98C), (30 second, 60C), and (30 second, 72C) profile in the thermocycler (based on purity)\n* P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", + "description": "This protocol is part five of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n Swift NGS Part 1 - Reverse Transcription and SPRI Cleanup\n Swift Rapid NGS Part 2 - Adaptase\n Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n Swift Rapid NGS Part 4 - SPRI Clean\nPart five of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nIndexing PCR\nSPRI Cleanup\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples that will be processed.\n PCR Mastermix Overage Percent: Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n Index Start Column: Specify which column on the index plate to begin aspirating from.\n Number of Thermocycler Cycles: Specify the number of repetitions samples will undergo a (20 second, 98C), (30 second, 60C), and (30 second, 72C) profile in the thermocycler (based on purity)\n P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", "internal": "6a93a2-part5", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 20\u00b5L Tips\nOpentrons 200uL Tips\nOpentrons 24-Tube Aluminum Block\nThermofisher Armadillo 96 Wellplate 200ul\n", "markdown": { diff --git a/protoBuilds/6a93a2/README.json b/protoBuilds/6a93a2/README.json index e12d68a97..c781bd65e 100644 --- a/protoBuilds/6a93a2/README.json +++ b/protoBuilds/6a93a2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol is one of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n* Swift Rapid NGS Part 2 - Adaptase\n* Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n* Swift Rapid NGS Part 4 - SPRI Clean\n* Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart one of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nReverse Transcription\nSPRI Cleanup\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples that will be processed.\n* Reverse Transcription Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n* Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n* Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n* P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", + "description": "This protocol is one of a five-part series to perform Swift Biosciences Rapid NGS Library Prep kit. The protocol is split in such a way so as to allow for the option to run between the Rapid and Standard versions of the kit. Please find all linked parts of the protocol below:\nLinks:\n Swift Rapid NGS Part 2 - Adaptase\n Swift Rapid NGS Part 3 - Extension, SPRI, and Ligation\n Swift Rapid NGS Part 4 - SPRI Clean\n Swift Rapid NGS Part 5 - Indexing and SPRI Clean\nPart one of this protocol is divided into the following methods for 8, 16, or 24 samples:\n\nReverse Transcription\nSPRI Cleanup\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples that will be processed.\n Reverse Transcription Mastermix Overage Percent (0-10%): Specify the percent overage of Reverse Transcription Mastermix to make and ultimately add to samples.\n Bead Drying Time: Specify the amount of time after both ethanol washes are completed and the plate is spun down to let the beads dry.\n Opentrons 96 Tip Rack 20ul Tip Type: Specify whether filter or non-filter 20ul tips will be employed.\n P300 Multi GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n P20 Single GEN2 Mount: Specify which mount (left or right) to load the P20 single channel pipette.\n", "internal": "6a93a2", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 20\u00b5L Tips\nOpentrons 200uL Tips\nOpentrons 24-Tube Aluminum Block\n", "markdown": { diff --git a/protoBuilds/6af807-amendment/README.json b/protoBuilds/6af807-amendment/README.json index 4b78ada07..66a61d448 100644 --- a/protoBuilds/6af807-amendment/README.json +++ b/protoBuilds/6af807-amendment/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: Mastermixes and cDNA tubes should be placed on their respective tube racks by column. Please look at the deck layout below for a full run (8 genes and 16 mastermixes).\n\n\n", - "description": "This protocol preps a 384 well plate for up to 8 cDNA samples in triplicates. The protocol can be broken down into 2 main parts:\n\ncDNA is added in triplicates down the column onto the plate.\nMastermix is added to the cDNA.\n\nExplanation of complex parameters below:\n* Number of cDNA: Specify the number of cDNA tubes that will be loaded onto the tube rack.\n* Number of mastermix tubes: Specify the number of mastermix tubes that will be added to the cDNA.\n* cDNA/mastermix volume: Specify the volume of both the cDNA and mastermix. Note, the mastermix volume will be calculated from this volume (total 20ul).\n* P20 Mount: Specify the mount (left or right) for the P20 single channel pipette.\n", + "description": "This protocol preps a 384 well plate for up to 8 cDNA samples in triplicates. The protocol can be broken down into 2 main parts:\n\ncDNA is added in triplicates down the column onto the plate.\nMastermix is added to the cDNA.\n\nExplanation of complex parameters below:\n Number of cDNA: Specify the number of cDNA tubes that will be loaded onto the tube rack.\n Number of mastermix tubes: Specify the number of mastermix tubes that will be added to the cDNA.\n cDNA/mastermix volume: Specify the volume of both the cDNA and mastermix. Note, the mastermix volume will be calculated from this volume (total 20ul).\n P20 Mount: Specify the mount (left or right) for the P20 single channel pipette.\n", "internal": "6af807", "labware": "\nThermofisher 384 well plate\nOpentrons 24 tube rack with 1.5mL Eppendorf tubes\nOpentrons 20ul Tips\n", "markdown": { diff --git a/protoBuilds/6af807/README.json b/protoBuilds/6af807/README.json index 6d330ec3c..7d1d18841 100644 --- a/protoBuilds/6af807/README.json +++ b/protoBuilds/6af807/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nNote: Mastermixes and cDNA tubes should be placed on their respective tube racks by column. Please look at the deck layout below for a full run (5 genes and 24 mastermixes).\n\n\n", - "description": "This protocol preps a 384 well plate for up to 5 cDNA samples in triplicates. The protocol can be broken down into 2 main parts:\n\ncDNA is added in triplicates down the column onto the plate.\nMastermix is added to the cDNA\n\nExplanation of complex parameters below:\n* Mastermix in triplicates across columns (new) or whole columns (original): Specify whether to run the new protocol (box method) or original protocol (which may break a box method).\n* Number of cDNA: Specify the number of cDNA tubes that will be loaded onto the tube rack.\n* Number of mastermix tubes: Specify the number of mastermix tubes that will be added to the cDNA.\n* Dispense Flow Rate: Specify the rate to dispense mastermix. A value of 1 is default, a value of 0.5 is half of the default value, and a value of 1.2 would be 20% higher than the default value, for example.\n* Blowout Flow Rate: Specify the rate to blowout mastermix. A value of 1 is default, a value of 0.5 is half of the default value, and a value of 1.2 would be 20% higher than the default value, for example.\n* cDNA/mastermix volume: Specify the volume of both the cDNA and mastermix. Note, the total volume of these two parameters should be equal to 20ul. \n* Reset Tipracks?: The OT-2 will track tips from run to run of the protocol (e.g. tip leaves off in H11 at the end of protocol 1; first tip pick up will be from H12 in Part 2). When tips run out for any particular run, the user will be prompted to replace all tip racks. The user will also have the option to \"Reset Tip Racks\" in the customized parameters section. Reset tip racks to pick up from A1 of the first tip rack of any one protocol.\n* P20 Mount: Specify the mount (left or right) for the P20 single channel pipette.\n", + "description": "This protocol preps a 384 well plate for up to 5 cDNA samples in triplicates. The protocol can be broken down into 2 main parts:\n\ncDNA is added in triplicates down the column onto the plate.\nMastermix is added to the cDNA\n\nExplanation of complex parameters below:\n Mastermix in triplicates across columns (new) or whole columns (original): Specify whether to run the new protocol (box method) or original protocol (which may break a box method).\n Number of cDNA: Specify the number of cDNA tubes that will be loaded onto the tube rack.\n Number of mastermix tubes: Specify the number of mastermix tubes that will be added to the cDNA.\n Dispense Flow Rate: Specify the rate to dispense mastermix. A value of 1 is default, a value of 0.5 is half of the default value, and a value of 1.2 would be 20% higher than the default value, for example.\n Blowout Flow Rate: Specify the rate to blowout mastermix. A value of 1 is default, a value of 0.5 is half of the default value, and a value of 1.2 would be 20% higher than the default value, for example.\n cDNA/mastermix volume: Specify the volume of both the cDNA and mastermix. Note, the total volume of these two parameters should be equal to 20ul. \n Reset Tipracks?: The OT-2 will track tips from run to run of the protocol (e.g. tip leaves off in H11 at the end of protocol 1; first tip pick up will be from H12 in Part 2). When tips run out for any particular run, the user will be prompted to replace all tip racks. The user will also have the option to \"Reset Tip Racks\" in the customized parameters section. Reset tip racks to pick up from A1 of the first tip rack of any one protocol.\n P20 Mount: Specify the mount (left or right) for the P20 single channel pipette.\n", "internal": "6af807", "labware": "\nThermofisher 384 well plate\nOpentrons 24 tube rack with 1.5mL Eppendorf tubes\nOpentrons 20ul Tips\nCustom Tip Rack\n", "markdown": { diff --git a/protoBuilds/6b9ee3/README.json b/protoBuilds/6b9ee3/README.json index 091db23ff..c630e4afa 100644 --- a/protoBuilds/6b9ee3/README.json +++ b/protoBuilds/6b9ee3/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol automates the creation of a mastermix (containing OptiMEM, DNA samples, and Viafect) and then dispenses this mastermix in triplicate. Using a simple CSV and a couple key parameters, this protocol can be easily adjusted for diifferent scenarios.\n\nThe protocol begins by adding 5.3\u00b5L of OptiMEM to the number of wells as defined by the user (the last well can receive more). After this, 4.4\u00b5L of DNA will be added to the wells per the CSV, transferring from sample tubes in deck slot 4 to the mastermix tubes in deck slot 5 (with OptiMEM). The OT-2 will then add 1.3\u00b5L of Viafect to the mastermix wells and pause until the user is ready to resume. After resuming, the OT-2 will transfer 10\u00b5L of the mastermix, in triplicate, to a 96-well plate in deck slot 6.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P20 Single-Channel Pipette\nOpentrons P20 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nOpentrons Aluminum Block Set\nOpentrons 4-in-1 Tube Rack Set\nCorning 96-Well Plate, 360\u00b5L Flat\n1.5mL Microcentrifuge Tube\nPCR Strips, 200\u00b5L\n\n\n\nDeck Setup\n\nSlot 1: Opentrons 20\u00b5L Tips\nSlot 2: Opentrons 20\u00b5L Tips\nSlot 3: Opentrons 20\u00b5L Tips\nSlot 4: Opentrons 96-Well Aluminum Block with PCR Strips containing samples/stock\nSlot 5: Opentrons 96-Well Aluminum Block with empty PCR Strips on the left for mastermix creation (columns 1-4) and a PCR Strip containing Viafect (column 12)\nSlot 6: Corning 96-Well Plate, 360\u00b5L Flat\nSlot 7: Opentrons 4-in-1 Tube Rack Set with a 1.5mL Microcentrifuge Tube containing OptiMEM in D6\n\nUsing the customizations field (below), set up your protocol.\n* Transfer CSV: Upload a CSV that will dictate the transfer of DNA from deck slot 4 to deck slot 5 (see below for more detail)\n* Number of Mastermix: Specify the number of mastermixes to be created (1-32).\n* Extra OptiMEM: Specify whether the last mastermix tube should receive 31.7\u00b5L of OptiMEM or the standard 5.3\u00b5L\n\n\nCSV Layout\n\n\n\nThe CSV should consist of two columns with headers, Source Well and Destination Well. Using capital letters, you can simply put well locations and the pipette will transfer 4.4\u00b5L from the source well (in deck slot 4) to the destination well (in deck slot 5).", + "description": "This protocol automates the creation of a mastermix (containing OptiMEM, DNA samples, and Viafect) and then dispenses this mastermix in triplicate. Using a simple CSV and a couple key parameters, this protocol can be easily adjusted for diifferent scenarios.\n\nThe protocol begins by adding 5.3\u00b5L of OptiMEM to the number of wells as defined by the user (the last well can receive more). After this, 4.4\u00b5L of DNA will be added to the wells per the CSV, transferring from sample tubes in deck slot 4 to the mastermix tubes in deck slot 5 (with OptiMEM). The OT-2 will then add 1.3\u00b5L of Viafect to the mastermix wells and pause until the user is ready to resume. After resuming, the OT-2 will transfer 10\u00b5L of the mastermix, in triplicate, to a 96-well plate in deck slot 6.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P20 Single-Channel Pipette\nOpentrons P20 Multi-Channel Pipette\nOpentrons 20\u00b5L Tips\nOpentrons Aluminum Block Set\nOpentrons 4-in-1 Tube Rack Set\nCorning 96-Well Plate, 360\u00b5L Flat\n1.5mL Microcentrifuge Tube\nPCR Strips, 200\u00b5L\n\n\n\nDeck Setup\n\nSlot 1: Opentrons 20\u00b5L Tips\nSlot 2: Opentrons 20\u00b5L Tips\nSlot 3: Opentrons 20\u00b5L Tips\nSlot 4: Opentrons 96-Well Aluminum Block with PCR Strips containing samples/stock\nSlot 5: Opentrons 96-Well Aluminum Block with empty PCR Strips on the left for mastermix creation (columns 1-4) and a PCR Strip containing Viafect (column 12)\nSlot 6: Corning 96-Well Plate, 360\u00b5L Flat\nSlot 7: Opentrons 4-in-1 Tube Rack Set with a 1.5mL Microcentrifuge Tube containing OptiMEM in D6\n\nUsing the customizations field (below), set up your protocol.\n Transfer CSV: Upload a CSV that will dictate the transfer of DNA from deck slot 4 to deck slot 5 (see below for more detail)\n Number of Mastermix: Specify the number of mastermixes to be created (1-32).\n* Extra OptiMEM: Specify whether the last mastermix tube should receive 31.7\u00b5L of OptiMEM or the standard 5.3\u00b5L\n\n\nCSV Layout\n\n\n\nThe CSV should consist of two columns with headers, Source Well and Destination Well. Using capital letters, you can simply put well locations and the pipette will transfer 4.4\u00b5L from the source well (in deck slot 4) to the destination well (in deck slot 5).", "internal": "6b9ee3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6bc986-part-2/README.json b/protoBuilds/6bc986-part-2/README.json index b51abfa00..0c1178fbc 100644 --- a/protoBuilds/6bc986-part-2/README.json +++ b/protoBuilds/6bc986-part-2/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "Part 2 of 6: Distribution of Prot K (Apostle)\nLinks:\n* Distribution of Sample Lysis Buffer\n* Distribution of Prot K (Apostle)\n* Transfer of DNA Template\n* Distribution of Master Mix\n* Distribution of Elution Buffer\n* Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the source well: 4 ul Prot K is distributed from a reservoir to the columns of a 96 deep-well plate with a blow out of the disposal volume occuring in a location close to the bottom of the reservoir.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", + "description": "Part 2 of 6: Distribution of Prot K (Apostle)\nLinks:\n Distribution of Sample Lysis Buffer\n Distribution of Prot K (Apostle)\n Transfer of DNA Template\n Distribution of Master Mix\n Distribution of Elution Buffer\n Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the source well: 4 ul Prot K is distributed from a reservoir to the columns of a 96 deep-well plate with a blow out of the disposal volume occuring in a location close to the bottom of the reservoir.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", "internal": "6bc986-part-2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6bc986-part-3/README.json b/protoBuilds/6bc986-part-3/README.json index 73b4a81de..33d8e1357 100644 --- a/protoBuilds/6bc986-part-3/README.json +++ b/protoBuilds/6bc986-part-3/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "Part 3 of 6: Transfer of DNA Template\nLinks:\n* Distribution of Sample Lysis Buffer\n* Distribution of Prot K (Apostle)\n* Transfer of DNA Template\n* Distribution of Master Mix\n* Distribution of Elution Buffer\n* Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python: 5 ul DNA template is transferred to the columns of a PCR plate.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", + "description": "Part 3 of 6: Transfer of DNA Template\nLinks:\n Distribution of Sample Lysis Buffer\n Distribution of Prot K (Apostle)\n Transfer of DNA Template\n Distribution of Master Mix\n Distribution of Elution Buffer\n Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python: 5 ul DNA template is transferred to the columns of a PCR plate.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", "internal": "6bc986-part-3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6bc986-part-4/README.json b/protoBuilds/6bc986-part-4/README.json index 5cff9180b..985c1e8e6 100644 --- a/protoBuilds/6bc986-part-4/README.json +++ b/protoBuilds/6bc986-part-4/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "Part 4 of 6: Distribution of Master Mix\nLinks:\n* Distribution of Sample Lysis Buffer\n* Distribution of Prot K (Apostle)\n* Transfer of DNA Template\n* Distribution of Master Mix\n* Distribution of Elution Buffer\n* Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the source reservoir well: 20 ul Master Mix is distributed from a reservoir with a blow out of the disposal volume occuring in a location close to the bottom of the source well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", + "description": "Part 4 of 6: Distribution of Master Mix\nLinks:\n Distribution of Sample Lysis Buffer\n Distribution of Prot K (Apostle)\n Transfer of DNA Template\n Distribution of Master Mix\n Distribution of Elution Buffer\n Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the source reservoir well: 20 ul Master Mix is distributed from a reservoir with a blow out of the disposal volume occuring in a location close to the bottom of the source well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", "internal": "6bc986-part-4", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6bc986-part-5/README.json b/protoBuilds/6bc986-part-5/README.json index 2c12d190a..745ffe5ac 100644 --- a/protoBuilds/6bc986-part-5/README.json +++ b/protoBuilds/6bc986-part-5/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "Part 5 of 6: Distribution of Elution Buffer\nLinks:\n* Distribution of Sample Lysis Buffer\n* Distribution of Prot K (Apostle)\n* Transfer of DNA Template\n* Distribution of Master Mix\n* Distribution of Elution Buffer\n* Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the source reservoir well: 20 ul elution buffer is distributed from a reservoir to the columns of a 96-well plate with a blow out of the disposal volume occuring in a location close to the bottom of the source well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", + "description": "Part 5 of 6: Distribution of Elution Buffer\nLinks:\n Distribution of Sample Lysis Buffer\n Distribution of Prot K (Apostle)\n Transfer of DNA Template\n Distribution of Master Mix\n Distribution of Elution Buffer\n Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the source reservoir well: 20 ul elution buffer is distributed from a reservoir to the columns of a 96-well plate with a blow out of the disposal volume occuring in a location close to the bottom of the source well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", "internal": "6bc986-part-5", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6bc986-part-6/README.json b/protoBuilds/6bc986-part-6/README.json index f3958965c..ed4738800 100644 --- a/protoBuilds/6bc986-part-6/README.json +++ b/protoBuilds/6bc986-part-6/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "Part 6 of 6: Distribution of Prot K (Qiagen)\nLinks:\n* Distribution of Sample Lysis Buffer\n* Distribution of Prot K (Apostle)\n* Transfer of DNA Template\n* Distribution of Master Mix\n* Distribution of Elution Buffer\n* Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the well: 10 ul sample lysis buffer is distributed from a reservoir to the columns of a 96 deep-well plate with a blow out occuring after each dispense in a location close to the bottom of the well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", + "description": "Part 6 of 6: Distribution of Prot K (Qiagen)\nLinks:\n Distribution of Sample Lysis Buffer\n Distribution of Prot K (Apostle)\n Transfer of DNA Template\n Distribution of Master Mix\n Distribution of Elution Buffer\n Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the well: 10 ul sample lysis buffer is distributed from a reservoir to the columns of a 96 deep-well plate with a blow out occuring after each dispense in a location close to the bottom of the well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", "internal": "6bc986-part-6", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6bc986/README.json b/protoBuilds/6bc986/README.json index 155c6f4cd..7b7e1ade4 100644 --- a/protoBuilds/6bc986/README.json +++ b/protoBuilds/6bc986/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "Part 1 of 6: Distribution of Sample Lysis Buffer\nLinks:\n* Distribution of Sample Lysis Buffer\n* Distribution of Prot K (Apostle)\n* Transfer of DNA Template\n* Distribution of Master Mix\n* Distribution of Elution Buffer\n* Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the well: 10 ul sample lysis buffer is distributed from a reservoir to the columns of a 96 deep-well plate with a blow out occurring after each dispense in a location close to the bottom of the well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", + "description": "Part 1 of 6: Distribution of Sample Lysis Buffer\nLinks:\n Distribution of Sample Lysis Buffer\n Distribution of Prot K (Apostle)\n Transfer of DNA Template\n Distribution of Master Mix\n Distribution of Elution Buffer\n Distribution of Prot K (Qiagen)\nThis protocol is a translation of the attached json protocol json protocol to python with a couple additional features for control of the blow out location in order to place it near the bottom of the well: 10 ul sample lysis buffer is distributed from a reservoir to the columns of a 96 deep-well plate with a blow out occurring after each dispense in a location close to the bottom of the well.\nThe deck layout can be displayed by uploading the attached json protocol to the Opentrons Protocol Designer web page.", "internal": "6bc986", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6be1f8/README.json b/protoBuilds/6be1f8/README.json index e9bdae994..2fee352a5 100644 --- a/protoBuilds/6be1f8/README.json +++ b/protoBuilds/6be1f8/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol preps 3, 384 well control plates for further testing of antibodies as part of a larger ELISA protocol. The protocol can be considered in 3 main parts:\n\nSerial dilution of antibody from stock\n96 well block prepped with diluent and mAb207 antibodies\n96 well block prepped with diluent and mAb210 antibodies\nTransfer of antibody to 3, 384 well control plates\n\nExplanation of complex parameters below:\n* Mix repetitions: Specify the number of mix repetitions.\n* Initial volume diluent tubes: Specify the initial volume in both diluent tubes. This is used for liquid height tracking.\n* P1000 aspirate/dispense flow rate: Specify the p1000 aspirate and dispense flow rates.\n* P1000 aspiration/dispense bottom clearance (mm): Specify the aspiration and dispense clearance from the bottom of the well for the P1000 pipette (to avoid plate pick up). The default value is 1mm from the bottom of the well.\n* Touch tip radius: Describes the proportion of the target well\u2019s radius. When radius=1.0, the pipette tip will move to the edge of the target well; when radius=0.5, it will move to 50% of the well\u2019s radius. Default: 1.0 (100%)\n* Touch tip v-offset: Specify the offset in mm from the top of the well to touch tip A positive offset moves the tip higher above the well, while a negative offset moves it lower into the well Default: -1.0 mm\n* Touch tip speed:Specify the speed for touch tip motion, in mm/s. Default: 60.0 mm/s, Max:80.0 mm/s, Min: 20.0 mm/s\n* P20 Pipette Mount: Specify which mount (left or right) to load your pipette.\n* P1000 Pipette Mount: Specify which mount (left or right) to load your pipette.\n", + "description": "This protocol preps 3, 384 well control plates for further testing of antibodies as part of a larger ELISA protocol. The protocol can be considered in 3 main parts:\n\nSerial dilution of antibody from stock\n96 well block prepped with diluent and mAb207 antibodies\n96 well block prepped with diluent and mAb210 antibodies\nTransfer of antibody to 3, 384 well control plates\n\nExplanation of complex parameters below:\n Mix repetitions: Specify the number of mix repetitions.\n Initial volume diluent tubes: Specify the initial volume in both diluent tubes. This is used for liquid height tracking.\n P1000 aspirate/dispense flow rate: Specify the p1000 aspirate and dispense flow rates.\n P1000 aspiration/dispense bottom clearance (mm): Specify the aspiration and dispense clearance from the bottom of the well for the P1000 pipette (to avoid plate pick up). The default value is 1mm from the bottom of the well.\n Touch tip radius: Describes the proportion of the target well\u2019s radius. When radius=1.0, the pipette tip will move to the edge of the target well; when radius=0.5, it will move to 50% of the well\u2019s radius. Default: 1.0 (100%)\n Touch tip v-offset: Specify the offset in mm from the top of the well to touch tip A positive offset moves the tip higher above the well, while a negative offset moves it lower into the well Default: -1.0 mm\n Touch tip speed:Specify the speed for touch tip motion, in mm/s. Default: 60.0 mm/s, Max:80.0 mm/s, Min: 20.0 mm/s\n P20 Pipette Mount: Specify which mount (left or right) to load your pipette.\n* P1000 Pipette Mount: Specify which mount (left or right) to load your pipette.\n", "internal": "6be1f8", "labware": "\nGreiner 384 well plate 200ul\nOpentrons 4-in-1 tube rack - 2x3 grid with Appleton 50mL tubes\nOpentrons 4-in-1 tube rack - 4x6 grid with Axygen 1.7mL tubes\nGreiner 96 well plate 2000ul\nOpentrons 20ul tip rack\nOpentrons 1000ul tip rack\n", "markdown": { diff --git a/protoBuilds/6c7447/README.json b/protoBuilds/6c7447/README.json index df862fe42..8435f27d8 100644 --- a/protoBuilds/6c7447/README.json +++ b/protoBuilds/6c7447/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol is an update to a qPCR prep protocol designed for the OT-1.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P300 Single-Channel Pipette\nOpentrons P10 Multi-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons 10\u00b5L Tips\nOpentrons 4-in-1 Tube Rack\nBio-Rad 96-Well Plate, 200\u00b5L\nEppendorf 2mL Tubes\nReagents\nSamples\n\n\n\nSlot 1: Bio-Rad Plate (qPCR Plate)\nSlot 2: Bio-Rad Plate (DNA Plate)\nSlot 3: Opentrons 10\u00b5L Tips, Full Tip Rack\nSlot 4: Tube Rack with 2mL Tubes and Reagents\nSlot 5: Opentrons 10\u00b5L Tips, with only tips in row 'A'\nSlot 6: [Opentrons 10\u00b5L Tips, with only tips in 'A1' and 'A2'\nSlot 7: Opentrons 300\u00b5L Tips, Full Tip Rack\nUsing the customizations fields, below set up your protocol.\n* P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\n* P300 Single Mount: Select which mount (left or right) the P300 Single is attached to.\n* Pre-Wet Tips?: Specify whether or not you'd like a mix step prior to each transfer to pre-wet the tip.\nNote: The tip racks in slot 5 and 6 should be empty, with tips only in row 'A'. This will allow the P10-Multi to effectively operate as a single channel pipette.", + "description": "This protocol is an update to a qPCR prep protocol designed for the OT-1.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P300 Single-Channel Pipette\nOpentrons P10 Multi-Channel Pipette\nOpentrons 300\u00b5L Tips\nOpentrons 10\u00b5L Tips\nOpentrons 4-in-1 Tube Rack\nBio-Rad 96-Well Plate, 200\u00b5L\nEppendorf 2mL Tubes\nReagents\nSamples\n\n\n\nSlot 1: Bio-Rad Plate (qPCR Plate)\nSlot 2: Bio-Rad Plate (DNA Plate)\nSlot 3: Opentrons 10\u00b5L Tips, Full Tip Rack\nSlot 4: Tube Rack with 2mL Tubes and Reagents\nSlot 5: Opentrons 10\u00b5L Tips, with only tips in row 'A'\nSlot 6: [Opentrons 10\u00b5L Tips, with only tips in 'A1' and 'A2'\nSlot 7: Opentrons 300\u00b5L Tips, Full Tip Rack\nUsing the customizations fields, below set up your protocol.\n P10 Multi Mount: Select which mount (left or right) the P10 Multi is attached to.\n P300 Single Mount: Select which mount (left or right) the P300 Single is attached to.\n* Pre-Wet Tips?: Specify whether or not you'd like a mix step prior to each transfer to pre-wet the tip.\nNote: The tip racks in slot 5 and 6 should be empty, with tips only in row 'A'. This will allow the P10-Multi to effectively operate as a single channel pipette.", "internal": "6c7447", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6cd9d6/README.json b/protoBuilds/6cd9d6/README.json index d6b252fb5..a787312b1 100644 --- a/protoBuilds/6cd9d6/README.json +++ b/protoBuilds/6cd9d6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Note: The deck setup changes throughout the course of the protocol. The initial calibration layout may differ from the final setup. Please follow the initial calibration setup and any instructions during the pauses.\n\nSlot 1: Temperature Module A + Bio Rad Plate (Sample Plate)\nSlot 2: Bio Rad Plate (Reagent #2 Plate)\nSlot 3: Temperature Module B + Bio Rad Plate (Reagent #1 Plate)\nSlot 4: Magnetic Module\nSlot 6: NEST 1 Well Reservoir (Ethanol Reservoir)\nSlot 7: Opentrons 200 uL Filter Tips\nSlot 8: Opentrons 200 uL Filter Tips\nSlot 10: Opentrons 20 uL Filter Tips\nSlot 11: Opentrons 20 uL Filter Tips\n\n", - "description": "This protocol performs a custom NGS Library Prep. It utilizes two temperature modules in Slot 1 and Slot 3 for the cooling of reagents. It also utilizes the magnetic module for bead based purification of samples.\nExplanation of complex parameters below:\n* P20 Multichannel GEN2 Mount Position: Choose the mount position of the P20 Multichannel GEN2 pipette.\n* P300 Multichannel GEN2 Mount Position: Choose the mount position of the P300 Multichannel GEN2 pipette.\n* Number of Samples: Enter total number of samples in the protocol run. Note: Because both pipettes are 8-channels, the number of samples should be a multiple of 8, otherwise it will use up additional tips for an entire column.\n", + "description": "This protocol performs a custom NGS Library Prep. It utilizes two temperature modules in Slot 1 and Slot 3 for the cooling of reagents. It also utilizes the magnetic module for bead based purification of samples.\nExplanation of complex parameters below:\n P20 Multichannel GEN2 Mount Position: Choose the mount position of the P20 Multichannel GEN2 pipette.\n P300 Multichannel GEN2 Mount Position: Choose the mount position of the P300 Multichannel GEN2 pipette.\n* Number of Samples: Enter total number of samples in the protocol run. Note: Because both pipettes are 8-channels, the number of samples should be a multiple of 8, otherwise it will use up additional tips for an entire column.\n", "internal": "6cd9d6", "labware": "\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nOpentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nNEST 12 Well Reservoir 15 mL\n", "markdown": { diff --git a/protoBuilds/6d7eb7/README.json b/protoBuilds/6d7eb7/README.json index f9fadc541..e1307659b 100644 --- a/protoBuilds/6d7eb7/README.json +++ b/protoBuilds/6d7eb7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nExample deck setup - tip racks loaded onto remining slots.\n\n\n", - "description": "Our most robust cherrypicking protocol. Specify aspiration height, labware, pipette, as well as source and destination wells with this all inclusive cherrypicking protocol.\n\nYour Transfer .csv File should be a .csv file formatted in the following way:\nPipette Mount to use,Source Labware,Source Slot,Source Well,Source Aspiration Height Above Bottom (in mm),Destination Well,Volume (in ul)\nleft,4x6 2ml screw true,1,A1,1,A11,1\nleft,4x6 1.5ml snap,1,A1,1,A5,3\nright,8x12 0.5ml snap,2,A1,1.5,H12,7\n...\nYou can also download a template here. Please making sure to include headers in your .csv file.\nYour source labware selection in the .csv file must be one of the following options, which correspond to the different sample tubes you use in your workflow:\n* 384 wellplate\n* 96 wellplate\n* 4x6 2ml screw true\n* 4x6 2ml screw false\n* 4x6 1.5ml snap\n* 4x6 1.5ml screw\n* 8x12 strip\n* 8x12 1ml plug\n* 8x12 0.5ml snap\nThe height offsets of different tubes seated in the same tuberack will be automatically calculated in the Python protocol logic. However, please ensure to calibrate your tuberacks with the following tube types in spot A1:\n* 4x6 Opentrons tuberack: 2ml screwcap false bottom in spot A1\n* 8x12 ThermoScientific Matrix tuberack: 1ml plugcap in spot A1\nCalibration to these tubes and tuberacks will allow for offsets to be properly taken into account during the protocol run.\n", + "description": "Our most robust cherrypicking protocol. Specify aspiration height, labware, pipette, as well as source and destination wells with this all inclusive cherrypicking protocol.\n\nYour Transfer .csv File should be a .csv file formatted in the following way:\nPipette Mount to use,Source Labware,Source Slot,Source Well,Source Aspiration Height Above Bottom (in mm),Destination Well,Volume (in ul)\nleft,4x6 2ml screw true,1,A1,1,A11,1\nleft,4x6 1.5ml snap,1,A1,1,A5,3\nright,8x12 0.5ml snap,2,A1,1.5,H12,7\n...\nYou can also download a template here. Please making sure to include headers in your .csv file.\nYour source labware selection in the .csv file must be one of the following options, which correspond to the different sample tubes you use in your workflow:\n 384 wellplate\n 96 wellplate\n 4x6 2ml screw true\n 4x6 2ml screw false\n 4x6 1.5ml snap\n 4x6 1.5ml screw\n 8x12 strip\n 8x12 1ml plug\n* 8x12 0.5ml snap\nThe height offsets of different tubes seated in the same tuberack will be automatically calculated in the Python protocol logic. However, please ensure to calibrate your tuberacks with the following tube types in spot A1:\n 4x6 Opentrons tuberack: 2ml screwcap false bottom in spot A1\n 8x12 ThermoScientific Matrix tuberack: 1ml plugcap in spot A1\nCalibration to these tubes and tuberacks will allow for offsets to be properly taken into account during the protocol run.\n", "internal": "6d7eb7", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6d7fc3-part-3/README.json b/protoBuilds/6d7fc3-part-3/README.json index 0e3de7d54..9d0f9910e 100644 --- a/protoBuilds/6d7fc3-part-3/README.json +++ b/protoBuilds/6d7fc3-part-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the starting deck layout for Part 3 (Cleanup of Adapter-ligated DNA with QIAact Beads).\n\n", - "description": "This protocol automates the third part of a seven part protocol for the GeneRead QIAact Lung DNA UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Adapter-ligated DNA with QIAact Beads part described in the GeneRead QIAact Lung DNA UMI Panel Handbook.\n\nPart 1: Fragmentation, End-repair and A-addition\nPart 2: Adapter Ligation\nPart 3: Cleanup of Adapter-ligated DNA with QIAact Beads.\nPart 4: Target Enrichment PCR\nPart 5: Cleanup of Target Enrichment PCR with QIAact Beads\nPart 6: Universal PCR Amplification.\nPart 7: Cleanup of Universal PCR with QIAact Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* Magnetic Module Engage Height (mm): The height the magnets should raise.\n", + "description": "This protocol automates the third part of a seven part protocol for the GeneRead QIAact Lung DNA UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Adapter-ligated DNA with QIAact Beads part described in the GeneRead QIAact Lung DNA UMI Panel Handbook.\n\nPart 1: Fragmentation, End-repair and A-addition\nPart 2: Adapter Ligation\nPart 3: Cleanup of Adapter-ligated DNA with QIAact Beads.\nPart 4: Target Enrichment PCR\nPart 5: Cleanup of Target Enrichment PCR with QIAact Beads\nPart 6: Universal PCR Amplification.\nPart 7: Cleanup of Universal PCR with QIAact Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n Magnetic Module Engage Height (mm): The height the magnets should raise.\n", "internal": "6d7fc3-part-3", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/6d7fc3-part-5/README.json b/protoBuilds/6d7fc3-part-5/README.json index 9a445acea..edd3ce302 100644 --- a/protoBuilds/6d7fc3-part-5/README.json +++ b/protoBuilds/6d7fc3-part-5/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the starting deck layout for Part 5 (Cleanup of Target Enrichment PCR with QIAact Beads).\n\n", - "description": "This protocol automates the fifth part of a seven part protocol for the GeneRead QIAact Lung DNA UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAact Beads part described in the GeneRead QIAact Lung DNA UMI Panel Handbook.\n\nPart 1: Fragmentation, End-repair and A-addition\nPart 2: Adapter Ligation\nPart 3: Cleanup of Adapter-ligated DNA with QIAact Beads.\nPart 4: Target Enrichment PCR\nPart 5: Cleanup of Target Enrichment PCR with QIAact Beads\nPart 6: Universal PCR Amplification.\nPart 7: Cleanup of Universal PCR with QIAact Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* Magnetic Module Engage Height (mm): The height the magnets should raise.\n", + "description": "This protocol automates the fifth part of a seven part protocol for the GeneRead QIAact Lung DNA UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Target Enrichment PCR with QIAact Beads part described in the GeneRead QIAact Lung DNA UMI Panel Handbook.\n\nPart 1: Fragmentation, End-repair and A-addition\nPart 2: Adapter Ligation\nPart 3: Cleanup of Adapter-ligated DNA with QIAact Beads.\nPart 4: Target Enrichment PCR\nPart 5: Cleanup of Target Enrichment PCR with QIAact Beads\nPart 6: Universal PCR Amplification.\nPart 7: Cleanup of Universal PCR with QIAact Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n Magnetic Module Engage Height (mm): The height the magnets should raise.\n", "internal": "6d7fc3-part-5", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/6d7fc3-part-7/README.json b/protoBuilds/6d7fc3-part-7/README.json index 7ee64f6fb..499213137 100644 --- a/protoBuilds/6d7fc3-part-7/README.json +++ b/protoBuilds/6d7fc3-part-7/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nThe example below illustrates the starting deck layout for Part 6 (Cleanup of Universal PCR with QIAact Beads).\n\n", - "description": "This protocol automates the seventh part of a seven part protocol for the GeneRead QIAact Lung DNA UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Universal PCR with QIAact Beads part described in the GeneRead QIAact Lung DNA UMI Panel Handbook.\n\nPart 1: Fragmentation, End-repair and A-addition\nPart 2: Adapter Ligation\nPart 3: Cleanup of Adapter-ligated DNA with QIAact Beads.\nPart 4: Target Enrichment PCR\nPart 5: Cleanup of Target Enrichment PCR with QIAact Beads\nPart 6: Universal PCR Amplification.\nPart 7: Cleanup of Universal PCR with QIAact Beads\n\nExplanation of complex parameters below:\n* Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n* P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n* Magnetic Module Engage Height (mm): The height the magnets should raise.\n", + "description": "This protocol automates the seventh part of a seven part protocol for the GeneRead QIAact Lung DNA UMI Panel Kit which constructs molecularly bar-coded DNA libraries for digital sequencing. This protocol automates the Cleanup of Universal PCR with QIAact Beads part described in the GeneRead QIAact Lung DNA UMI Panel Handbook.\n\nPart 1: Fragmentation, End-repair and A-addition\nPart 2: Adapter Ligation\nPart 3: Cleanup of Adapter-ligated DNA with QIAact Beads.\nPart 4: Target Enrichment PCR\nPart 5: Cleanup of Target Enrichment PCR with QIAact Beads\nPart 6: Universal PCR Amplification.\nPart 7: Cleanup of Universal PCR with QIAact Beads\n\nExplanation of complex parameters below:\n Number of Samples: The total number of DNA samples. Samples must range between 1 (minimum) and 12 (maximum).\n P300 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n P20 Single GEN2 Pipette Mount Position: The position of the pipette, either left or right.\n Magnetic Module Engage Height (mm): The height the magnets should raise.\n", "internal": "6d7fc3-part-7", "labware": "\nOpentrons Filter Tips\nNEST 96 Well 100 uL PCR Plate\nOpentrons Aluminum Block Set\n", "markdown": { diff --git a/protoBuilds/6d901d/README.json b/protoBuilds/6d901d/README.json index 1afb18575..f6934fe5a 100644 --- a/protoBuilds/6d901d/README.json +++ b/protoBuilds/6d901d/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Example deck setup starting state, note that the cherry picking plate in slot 8 is a place-holder and is used in the optional 2nd part of the protocol. The different colors on the normalization plate wells illustrates samples with different concentrations before being normalized.\n\n* Well A1 on the reservoir on slot 9: Diluent, e.g. water or buffer.", - "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library preparation. With this protocol, you can easily normalize the concentrations of samples in a 96 or 384 microwell plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol. This protocol is a modified version of our Normalization Protocol, that instead uses a multi-channel pipette as single channel pipette by picking up one tip at a time.\nThere is an optional Part 2: Cherrypicking Protocol to this protocol which performs cherrypicking using a multi-channel pipette in the same way.\nNote: This protocol was updated for a change in our software stack and will require app 6.0 or greater.\nUsing the customization fields below, set up your protocol.\n* Volumes CSV: Your input CSV specifying the normalization volumes. See the Setup section below for details.\n* P300 Multi Mount: Select mount for P300 Multi-Channel Pipette\n* P20 Multi Mount: Select mount for P20 Multi-Channel Pipette\n* Plate Type: Select the model of microwell plate to normalize samples on.\n* Reservoir Type: The type of the diluent reservoir. If you are selecting a multi-well reservoir you should place your diluent in well A1.\n* Use Filter Tips?: Select whether your pipette will use regular or filter tips.\n* Tip Usage Strategy: You can select whether your pipette will reuse the same tip throughout the entire normalization procedure or change tips after every diluent transfer.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.4.0 or later)\nOpentrons Multi-Channel Pipette and corresponding Tips\nSamples in a compatible plate (96-well or 384-well)\nAutomation-friendly reservoir\nDiluent\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nCSV Format\nYour file must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). It should be formatted in \u201clandscape\u201d orientation, with the value corresponding to well A1 in the upper left-hand corner of the value list.\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, etc.\nIf you would like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV from there.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).", + "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library preparation. With this protocol, you can easily normalize the concentrations of samples in a 96 or 384 microwell plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol. This protocol is a modified version of our Normalization Protocol, that instead uses a multi-channel pipette as single channel pipette by picking up one tip at a time.\nThere is an optional Part 2: Cherrypicking Protocol to this protocol which performs cherrypicking using a multi-channel pipette in the same way.\nNote: This protocol was updated for a change in our software stack and will require app 6.0 or greater.\nUsing the customization fields below, set up your protocol.\n Volumes CSV: Your input CSV specifying the normalization volumes. See the Setup section below for details.\n P300 Multi Mount: Select mount for P300 Multi-Channel Pipette\n P20 Multi Mount: Select mount for P20 Multi-Channel Pipette\n Plate Type: Select the model of microwell plate to normalize samples on.\n Reservoir Type: The type of the diluent reservoir. If you are selecting a multi-well reservoir you should place your diluent in well A1.\n Use Filter Tips?: Select whether your pipette will use regular or filter tips.\n* Tip Usage Strategy: You can select whether your pipette will reuse the same tip throughout the entire normalization procedure or change tips after every diluent transfer.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.4.0 or later)\nOpentrons Multi-Channel Pipette and corresponding Tips\nSamples in a compatible plate (96-well or 384-well)\nAutomation-friendly reservoir\nDiluent\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nCSV Format\nYour file must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). It should be formatted in \u201clandscape\u201d orientation, with the value corresponding to well A1 in the upper left-hand corner of the value list.\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, etc.\nIf you would like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV from there.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).", "internal": "6d901d", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6e160e/README.json b/protoBuilds/6e160e/README.json index 3da0f48d0..802c1cb29 100644 --- a/protoBuilds/6e160e/README.json +++ b/protoBuilds/6e160e/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSamples are layed out between plates in the following manner:\n\n", - "description": "This protocol preps a 384 well plate on the temperature module with reaction mix and sample. Reaction mix is held in well one of a 12 well reservoir on the temperature module. Both temperature modules are held at 4C. The protocol uses a multi-channel to fill full plates, and a single channel to fill the last unfilled plate. Samples and reaction mix are filled by row, skipping columns.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples for this run.\n* P20 Mounts: Specify which mount (left or right) for each the P20 Single-Channel and P20 Multi-Channel pipettes.\n", + "description": "This protocol preps a 384 well plate on the temperature module with reaction mix and sample. Reaction mix is held in well one of a 12 well reservoir on the temperature module. Both temperature modules are held at 4C. The protocol uses a multi-channel to fill full plates, and a single channel to fill the last unfilled plate. Samples and reaction mix are filled by row, skipping columns.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples for this run.\n P20 Mounts: Specify which mount (left or right) for each the P20 Single-Channel and P20 Multi-Channel pipettes.\n", "internal": "6e160e", "labware": "\nCorning 384 Well Plate 112 \u00b5L Flat\nOpentrons 20\u00b5L Filter Tips\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 12-Well Reservoirs, 15 mL\n", "markdown": { diff --git a/protoBuilds/6e2509/README.json b/protoBuilds/6e2509/README.json index 206b3bfe9..b22bd5695 100644 --- a/protoBuilds/6e2509/README.json +++ b/protoBuilds/6e2509/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol automates the transfer of PCR mix and samples from up to four 96-well elution plates to a 384-well plate. It follows a specific format detailed in the image below. Columns from the 96 well elution plates correspond to specific wells on the 384 well plate. Each elution plate contains a control that is also transferred into the 384-well plate. For runs that have less than four plates, the controls will need to be added manually for the corresponding elution plate.\n96 Well Elution Plate Format:\n\n384 Well Plate Format:\n\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermofisher 384 well optical PCR plate\nMolgen 96 Well Elution Plate\nOpentrons NEST 12-Well Reservoir\n\n\n\nFor this protocol, be sure that the P20 pipette is attached.\nUsing the customization fields below, set up your protocol.\n* P20 Multichannel Mount: Choose the mount position of your P20 multichannel pipette.\n* Number of samples: Input the total number of samples in all four plates. Supports up to 384 samples.\n* PCR Mix Transfer Volume: Input the volume of PCR mix to transfer per well. Default is 7.5 uL.\n* Sample Transfer Volume: Input the volume of sample to transfer per well. Default is 5 uL.\n* Sample Aspiration Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will aspirate.\n* Sample Dispensing Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will dispense.\n* Master Mix Aspiration Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will aspirate.\n* Master Mix Dispensing Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will dispense.\nNote About Reagents:\nPCR Mix should be placed into column A1 of the 96 well plate.\nLabware Setup\nSlot 1: Plate 1\nSlot 2: Plate 2\nSlot 4: Plate 3\nSlot 5: Plate 4\nSlot 3: 384 Well PCR Plate\nSlot 6: 96 Well Plate (PCR Mix in Column A1)\nSlots 7 - 11: Opentrons 96 Filter Tip Rack 20 uL", + "description": "This protocol automates the transfer of PCR mix and samples from up to four 96-well elution plates to a 384-well plate. It follows a specific format detailed in the image below. Columns from the 96 well elution plates correspond to specific wells on the 384 well plate. Each elution plate contains a control that is also transferred into the 384-well plate. For runs that have less than four plates, the controls will need to be added manually for the corresponding elution plate.\n96 Well Elution Plate Format:\n\n384 Well Plate Format:\n\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermofisher 384 well optical PCR plate\nMolgen 96 Well Elution Plate\nOpentrons NEST 12-Well Reservoir\n\n\n\nFor this protocol, be sure that the P20 pipette is attached.\nUsing the customization fields below, set up your protocol.\n P20 Multichannel Mount: Choose the mount position of your P20 multichannel pipette.\n Number of samples: Input the total number of samples in all four plates. Supports up to 384 samples.\n PCR Mix Transfer Volume: Input the volume of PCR mix to transfer per well. Default is 7.5 uL.\n Sample Transfer Volume: Input the volume of sample to transfer per well. Default is 5 uL.\n Sample Aspiration Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will aspirate.\n Sample Dispensing Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will dispense.\n Master Mix Aspiration Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will aspirate.\n Master Mix Dispensing Height Above Bottom of the Well: Specify the height from the bottom of the well in which the pipette will dispense.\nNote About Reagents:\nPCR Mix should be placed into column A1 of the 96 well plate.\nLabware Setup\nSlot 1: Plate 1\nSlot 2: Plate 2\nSlot 4: Plate 3\nSlot 5: Plate 4\nSlot 3: 384 Well PCR Plate\nSlot 6: 96 Well Plate (PCR Mix in Column A1)\nSlots 7 - 11: Opentrons 96 Filter Tip Rack 20 uL", "internal": "6e2509", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6f4e2c/README.json b/protoBuilds/6f4e2c/README.json index 924e7b971..5c02a7e3f 100644 --- a/protoBuilds/6f4e2c/README.json +++ b/protoBuilds/6f4e2c/README.json @@ -5,7 +5,7 @@ "Blood Sample" ] }, - "description": "This protocol automates the protocol from Sileks for DNA isolation from whole blood with MP@SiO2 magnetic particles. This protocol utilizes a P300-Multi Channel pipette and gives the user the option to select either 24 or 48 samples and whether to dispense liquid waste in a reservoir in slot 8 or in the fixed trash container. This protocol is also designed for using the Eppendorf 1000\u00b5L deep-well plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons Temperature Module\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips or Opentrons 200\u00b5L Filter Tips\nBio-Rad 96-Well Plate, 200\u00b5L\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL, if using for liquid waste\nEppendorf 1000\u00b5L Deep-Well Plate\nReagents\nSamples\n\n\n\nSlot 1: Opentrons Magnetic Module with Eppendorf Deep-Well Plate and 100\u00b5L of blood sample in corresponding wells (either 24 or 48)\nSlot 2: NEST 12-Well Reservoir, 15mL\n* A1: Start Buffer\n* A2: Lysis/Binding Buffer\n* A3: Lysis/Binding Buffer (48 Samples)\n* A4: Wash Buffer 1\n* A5: Wash Buffer 1 (48 Samples)\n* A6: Wash Buffer 2\n* A7: Wash Buffer 2 (48 Samples)\n* A8: Wash Buffer 3\n* A9: Wash Buffer 3 (48 Samples)\n* A10: Elution Buffer\nSlot 3: Opentrons Tips\nSlot 4: Opentrons Temperature Module\nSlot 5: Bio-Rad 96-Well Plate, 200\u00b5L, for final elution\nSlot 6: Opentrons Tips\nSlot 8: NEST 1-Well Reservoir, 195mL, if using for liquid waste\nSlot 9: Opentrons Tips\nSlot 10: Opentrons Tips\nSlot 11: Opentrons Tips\nUsing the customizations fields, below set up your protocol.\n* P300 Multi Mount: Select which mount (left or right) the P300 Multi is attached to.\n* Tip Type: Select the type of tips for this protocol (non/filter).\n* Number of Samples: Specify the number of samples you'd like to run.\n* Liquid Waste in Reservoir: Specify if liquid waste should be dispensed in reservoir (or fixed trash container)", + "description": "This protocol automates the protocol from Sileks for DNA isolation from whole blood with MP@SiO2 magnetic particles. This protocol utilizes a P300-Multi Channel pipette and gives the user the option to select either 24 or 48 samples and whether to dispense liquid waste in a reservoir in slot 8 or in the fixed trash container. This protocol is also designed for using the Eppendorf 1000\u00b5L deep-well plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons Temperature Module\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50/300\u00b5L Tips or Opentrons 200\u00b5L Filter Tips\nBio-Rad 96-Well Plate, 200\u00b5L\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL, if using for liquid waste\nEppendorf 1000\u00b5L Deep-Well Plate\nReagents\nSamples\n\n\n\nSlot 1: Opentrons Magnetic Module with Eppendorf Deep-Well Plate and 100\u00b5L of blood sample in corresponding wells (either 24 or 48)\nSlot 2: NEST 12-Well Reservoir, 15mL\n A1: Start Buffer\n A2: Lysis/Binding Buffer\n A3: Lysis/Binding Buffer (48 Samples)\n A4: Wash Buffer 1\n A5: Wash Buffer 1 (48 Samples)\n A6: Wash Buffer 2\n A7: Wash Buffer 2 (48 Samples)\n A8: Wash Buffer 3\n A9: Wash Buffer 3 (48 Samples)\n A10: Elution Buffer\nSlot 3: Opentrons Tips\nSlot 4: Opentrons Temperature Module\nSlot 5: Bio-Rad 96-Well Plate, 200\u00b5L, for final elution\nSlot 6: Opentrons Tips\nSlot 8: NEST 1-Well Reservoir, 195mL, if using for liquid waste\nSlot 9: Opentrons Tips\nSlot 10: Opentrons Tips\nSlot 11: Opentrons Tips\nUsing the customizations fields, below set up your protocol.\n P300 Multi Mount: Select which mount (left or right) the P300 Multi is attached to.\n Tip Type: Select the type of tips for this protocol (non/filter).\n Number of Samples: Specify the number of samples you'd like to run.\n Liquid Waste in Reservoir: Specify if liquid waste should be dispensed in reservoir (or fixed trash container)", "internal": "6f4e2c", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6faa1e/README.json b/protoBuilds/6faa1e/README.json index 0d50a34af..896a36100 100644 --- a/protoBuilds/6faa1e/README.json +++ b/protoBuilds/6faa1e/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This protocol automates the steps of transferring mastermix from source plates to destination plates.\n\n\n\nP20 multi-channel GEN2 electronic pipette\nOpentrons 20ul tiprack\nThermo Scientific\u2122 PCR Plate, 96-well, semi-skirted\nEppendorf PCR cooler\n\n\n\nDeck Setup\n* Destination Plates (PCR Plate on top of Eppendorf Cooler) (Slots 1-8)\n* Source Plate (NEST 12-channel 15ml reservoir on top of ice tray) (Slot 11)\n* Opentrons 20 uL tip rack (Slot 10)", + "description": "This protocol automates the steps of transferring mastermix from source plates to destination plates.\n\n\n\nP20 multi-channel GEN2 electronic pipette\nOpentrons 20ul tiprack\nThermo Scientific\u2122 PCR Plate, 96-well, semi-skirted\nEppendorf PCR cooler\n\n\n\nDeck Setup\n Destination Plates (PCR Plate on top of Eppendorf Cooler) (Slots 1-8)\n Source Plate (NEST 12-channel 15ml reservoir on top of ice tray) (Slot 11)\n* Opentrons 20 uL tip rack (Slot 10)", "internal": "6faa1e", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6fe477-workflow-1/README.json b/protoBuilds/6fe477-workflow-1/README.json index 9e306a2e0..33f8c5cea 100644 --- a/protoBuilds/6fe477-workflow-1/README.json +++ b/protoBuilds/6fe477-workflow-1/README.json @@ -5,7 +5,7 @@ "Nucleic Acid Purification" ] }, - "description": "This protocol automates variable pooling of samples and addition of lysis buffer for automated extraction downstream. \nWorkflow 2\n\n\n\nP300 single-channel GEN2 electronic pipette\nP300 multi-channel GEN2 electronic pipette\nOpentrons 200ul filter tiprack\nOpentrons 300ul tiprack\nNunc\u2122 96-Well Polypropylene DeepWell\u2122 Storage Plates\nCaplugs\u2122 30mL Centrifuge Tubes\n\n\n\nDeck Setup\n* Opentrons 200ul filter tiprack (Slot 5)\n* Opentrons 300ul tiprack (Slot 6)\n* Deep Well Plate (Slot 2)\n* NEST 195 mL Reservoir (Slot 3)\n* 30 mL Caplug Tubes in Opentrons 6 Tube Rack (Slots 1, 4, 7, 8, 9, 10, 11)", + "description": "This protocol automates variable pooling of samples and addition of lysis buffer for automated extraction downstream. \nWorkflow 2\n\n\n\nP300 single-channel GEN2 electronic pipette\nP300 multi-channel GEN2 electronic pipette\nOpentrons 200ul filter tiprack\nOpentrons 300ul tiprack\nNunc\u2122 96-Well Polypropylene DeepWell\u2122 Storage Plates\nCaplugs\u2122 30mL Centrifuge Tubes\n\n\n\nDeck Setup\n Opentrons 200ul filter tiprack (Slot 5)\n Opentrons 300ul tiprack (Slot 6)\n Deep Well Plate (Slot 2)\n NEST 195 mL Reservoir (Slot 3)\n* 30 mL Caplug Tubes in Opentrons 6 Tube Rack (Slots 1, 4, 7, 8, 9, 10, 11)", "internal": "6fe477", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6fe477-workflow-2/README.json b/protoBuilds/6fe477-workflow-2/README.json index 5b0a46ada..986174f6f 100644 --- a/protoBuilds/6fe477-workflow-2/README.json +++ b/protoBuilds/6fe477-workflow-2/README.json @@ -5,7 +5,7 @@ "Nucleic Acid Purification" ] }, - "description": "This protocol automates variable pooling of samples and addition of lysis buffer for manual extraction downstream. \nWorkflow 1\n\n\n\nP300 single-channel GEN2 electronic pipette\nP1000 single-channel GEN2 electronic pipette\nOpentrons 200ul filter tiprack\nOpentrons 1000ul tiprack\nVWR 1.5mL Centrifuge\n\n\n\nDeck Setup\n* Opentrons 200ul filter tiprack (Slot 5)\n* Opentrons 1000ul tiprack (Slot 6)\n* VWR 1.5mL Tubes in Opentrons 24 Tube Rack (Slot 2)\n* NEST 195 mL Reservoir (Slot 3)\n* 30 mL Caplug Tubes in Opentrons 6 Tube Rack (Slots 1, 4, 7, 8, 9, 10, 11)", + "description": "This protocol automates variable pooling of samples and addition of lysis buffer for manual extraction downstream. \nWorkflow 1\n\n\n\nP300 single-channel GEN2 electronic pipette\nP1000 single-channel GEN2 electronic pipette\nOpentrons 200ul filter tiprack\nOpentrons 1000ul tiprack\nVWR 1.5mL Centrifuge\n\n\n\nDeck Setup\n Opentrons 200ul filter tiprack (Slot 5)\n Opentrons 1000ul tiprack (Slot 6)\n VWR 1.5mL Tubes in Opentrons 24 Tube Rack (Slot 2)\n NEST 195 mL Reservoir (Slot 3)\n* 30 mL Caplug Tubes in Opentrons 6 Tube Rack (Slots 1, 4, 7, 8, 9, 10, 11)", "internal": "6fe477", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/6ff9e9/README.json b/protoBuilds/6ff9e9/README.json index 47cc60d96..a4d8c4e94 100644 --- a/protoBuilds/6ff9e9/README.json +++ b/protoBuilds/6ff9e9/README.json @@ -5,7 +5,7 @@ "Nucleic Acid Extraction" ] }, - "description": "This is a flexible protocol accommodating various nucleic acid purifications. The protocol is broken down into 5 main parts:\n* binding buffer and magnetic beads addition to samples\n* bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nLysed samples should be loaded on the magnetic module in a NEST 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nOpentrons temperature module\nCustom 2-channel 170ml reservoirs\nCustom 96 Well Plate 200 \u00b5L PCR\nNEST 96 Deepwell Plate 2mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\nSlots 11, 8, 5, and 2, from top to bottom:\n", + "description": "This is a flexible protocol accommodating various nucleic acid purifications. The protocol is broken down into 5 main parts:\n binding buffer and magnetic beads addition to samples\n bead wash 2x using magnetic module\n* final elution to chilled PCR plate\nLysed samples should be loaded on the magnetic module in a NEST 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nOpentrons temperature module\nCustom 2-channel 170ml reservoirs\nCustom 96 Well Plate 200 \u00b5L PCR\nNEST 96 Deepwell Plate 2mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\nSlots 11, 8, 5, and 2, from top to bottom:\n", "internal": "6ffe9", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/701319/README.json b/protoBuilds/701319/README.json index 9101c207f..d3975f0ad 100644 --- a/protoBuilds/701319/README.json +++ b/protoBuilds/701319/README.json @@ -5,7 +5,7 @@ "Mass Spec" ] }, - "description": "This protocol performs a custom mass spectrometry sample prep for peptides up to 48 samples.\n\n\n\nOpentrons Magnetic Module\nNEST 96-well PCR plate 100\u00b5l full skirt\nOpentrons 20\u00b5l tiprack\nOpentrons 300\u00b5l tiprack\nOpentrons P20 and P300 GEN2 multi-channel electronic pipette\n\n\n\nDeck Setup\n* Nunc 96-well polystyrene V-bottom microwell plate (Slot 1)\n* NEST 0.1 mL 96-Well PCR Plate, Full Skirt (Slot 2)\n* NEST 12-well reservoir, 15 mL,Opentrons (Slot 3)\n* Opentrons Magnetic Module GEN2 (Slot 4)\n* Stellar Scientific Cluster Tubes Racked, 1.2 mL (Slot 4, On Magnetic Module)\n* Opentrons 300 uL Tip Rack (Slot 5, Slot 8)\n* Opentrons 20 uL Tip Rack (Slot 6, Slot 9)\nNOTE: Switch the Cluster Tubes Plate with the NEST PCR Plate on the Magnetic Module once the Pause step is reached.\nMagnetic Module Engage Height from Well Bottom (mm) refers to the height the magnet will move to from the bottom of the well. A value of 13.5 mm will move the tops of the magnets to level with that height value.", + "description": "This protocol performs a custom mass spectrometry sample prep for peptides up to 48 samples.\n\n\n\nOpentrons Magnetic Module\nNEST 96-well PCR plate 100\u00b5l full skirt\nOpentrons 20\u00b5l tiprack\nOpentrons 300\u00b5l tiprack\nOpentrons P20 and P300 GEN2 multi-channel electronic pipette\n\n\n\nDeck Setup\n Nunc 96-well polystyrene V-bottom microwell plate (Slot 1)\n NEST 0.1 mL 96-Well PCR Plate, Full Skirt (Slot 2)\n NEST 12-well reservoir, 15 mL,Opentrons (Slot 3)\n Opentrons Magnetic Module GEN2 (Slot 4)\n Stellar Scientific Cluster Tubes Racked, 1.2 mL (Slot 4, On Magnetic Module)\n Opentrons 300 uL Tip Rack (Slot 5, Slot 8)\n* Opentrons 20 uL Tip Rack (Slot 6, Slot 9)\nNOTE: Switch the Cluster Tubes Plate with the NEST PCR Plate on the Magnetic Module once the Pause step is reached.\nMagnetic Module Engage Height from Well Bottom (mm) refers to the height the magnet will move to from the bottom of the well. A value of 13.5 mm will move the tops of the magnets to level with that height value.", "internal": "701319", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/70567f/README.json b/protoBuilds/70567f/README.json index a2a6476f8..2afa263f6 100644 --- a/protoBuilds/70567f/README.json +++ b/protoBuilds/70567f/README.json @@ -5,7 +5,7 @@ "Ampure XP" ] }, - "description": "This protocol performs a custom NGS library prep cleanup using Ampure XP beads in a variable ratio with samples. The samples are mounted on an Opentrons magnetic module, and the final elute is transferred to a fresh PCR plate.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n\n\n\nOpentrons Magnetic Module (GEN2)\nNEST 96 Deepwell Plate 2mL\nP300 multi-channel electronic pipette (GEN2)\nOpentrons 200ul filtertipracks\n\n\n\n96-deepwell plate (slot 7)\n* column 1: Ampure XP beads\n* column 2: 80% ethanol\n* column 3: EB buffer\n* columns 10-12: liquid waste (loaded empty at start)", + "description": "This protocol performs a custom NGS library prep cleanup using Ampure XP beads in a variable ratio with samples. The samples are mounted on an Opentrons magnetic module, and the final elute is transferred to a fresh PCR plate.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n\n\n\nOpentrons Magnetic Module (GEN2)\nNEST 96 Deepwell Plate 2mL\nP300 multi-channel electronic pipette (GEN2)\nOpentrons 200ul filtertipracks\n\n\n\n96-deepwell plate (slot 7)\n column 1: Ampure XP beads\n column 2: 80% ethanol\n column 3: EB buffer\n columns 10-12: liquid waste (loaded empty at start)", "internal": "70567f", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7062c9-2/README.json b/protoBuilds/7062c9-2/README.json index 9a0835fa6..dbaf15184 100644 --- a/protoBuilds/7062c9-2/README.json +++ b/protoBuilds/7062c9-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "This example starting deck state shows the layout for 24 samples:\n\n\npink on starting sample plate: 110\u00b5l annealed and digested samples\ngreen on reagent reservoir: buffer 2 (wash buffer)\nblue on reagent reservoir: water\npurple on reagent reservoir: magnetic beads\norange on reagent reservoir: buffer 3 (elution buffer)\n\n", - "description": "Links:\n* Steps 1-2 (annealing preparation and digestion)\n* Steps 3-6 (extraction)\nThis is a flexible protocol accommodating a multi-step nucleic acid extraction. The protocol is broken down into the following main parts:\n* magnetic beads pre-wash\n* beads binding to sample\n* beads washing\n* final elution\nBefore running the protocol, 100\u00b5l of beads in buffer should be pre-loaded on the magnetic module in a NEST 96-deepwell plate. For reagent layout, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", + "description": "Links:\n Steps 1-2 (annealing preparation and digestion)\n Steps 3-6 (extraction)\nThis is a flexible protocol accommodating a multi-step nucleic acid extraction. The protocol is broken down into the following main parts:\n magnetic beads pre-wash\n beads binding to sample\n beads washing\n final elution\nBefore running the protocol, 100\u00b5l of beads in buffer should be pre-loaded on the magnetic module in a NEST 96-deepwell plate. For reagent layout, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n", "internal": "7062c9", "labware": "\nNEST 12 Well Reservoir 15 mL\nNEST 1 Well Reservoir 195 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nNEST 96 Deepwell Plate 2mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n", "markdown": { diff --git a/protoBuilds/7062c9/README.json b/protoBuilds/7062c9/README.json index 9f59c6733..92f306bd0 100644 --- a/protoBuilds/7062c9/README.json +++ b/protoBuilds/7062c9/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "This example starting deck state shows the layout for 24 samples:\n\n\ngreen on sample tuberack: starting samples\nblue on reagent reservoir: water\npink on buffer + probe tuberack: buffer\npurple on buffer + probe tuberack: protease\norange buffer + probe tuberack: available spots for probes\n\n", - "description": "Links:\n* Steps 1-2 (annealing preparation and digestion)\n* Steps 3-6 (extraction)\nThis is a flexible normalization protocol accommodating sample annealing preparation and digestion pre- and post-PCR. Normalization parameters should be input as a .csv file below, and should be formatted as shown in the following template:\nsample conc. (mg/ml),sample volume (\u00b5l),water volume (\u00b5l),buffer 1 (\u00b5l),probe volume (\u00b5l),probe tube location (C1-D6),total volume (\u00b5l)\n1,40,50,10,5,A3,105\n2.2,18.2,71.8,10,5,A3,105\n2.03,19.7,70.3,10,5,A4,105\nFor sample traceability and consistency, samples are mapped directly from the sample plate (slot 1) to the final normalized plate (slot 2). Sample plate well A1 is transferred to normalized plate A1, Sample plate well B1 to normalized plate B1, ..., D2 to D2, etc.\n", + "description": "Links:\n Steps 1-2 (annealing preparation and digestion)\n Steps 3-6 (extraction)\nThis is a flexible normalization protocol accommodating sample annealing preparation and digestion pre- and post-PCR. Normalization parameters should be input as a .csv file below, and should be formatted as shown in the following template:\nsample conc. (mg/ml),sample volume (\u00b5l),water volume (\u00b5l),buffer 1 (\u00b5l),probe volume (\u00b5l),probe tube location (C1-D6),total volume (\u00b5l)\n1,40,50,10,5,A3,105\n2.2,18.2,71.8,10,5,A3,105\n2.03,19.7,70.3,10,5,A4,105\nFor sample traceability and consistency, samples are mapped directly from the sample plate (slot 1) to the final normalized plate (slot 2). Sample plate well A1 is transferred to normalized plate A1, Sample plate well B1 to normalized plate B1, ..., D2 to D2, etc.\n", "internal": "7062c9", "labware": "\nNEST 12 Well Reservoir 15 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nOpentrons 24 Tube Rack with NEST 1.5 mL Screwcap Tubes or equivalent\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { diff --git a/protoBuilds/71381b/README.json b/protoBuilds/71381b/README.json index b53f8b072..589e84ef0 100644 --- a/protoBuilds/71381b/README.json +++ b/protoBuilds/71381b/README.json @@ -5,7 +5,7 @@ "Zymo Kit" ] }, - "description": "This protocol automates the Zymo Quick-DNA HMW MagBead Kit with an additional labelling step that takes place before the purification.\n\nThe parameter section below gives you the ability to select either the Labelling portion of the protocol or the Purification portion of the protocol (you can select both). During the labelling portion, MilliQ Water, CSB, M.Taql, MTC22, and Proteinase K are added to the samples and the samples incubate while on the Temperature Module. During the purification portion, the samples are purified using the Zymo MagBead Kit in conjunction with Opentrons Magnetic Module.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nOpentrons Temperatue Module, GEN2\nOpentrons Magnetic Module, GEN2\nOpentrons P20 8-Channel Pipette\nOpentrons P300 8-Channel Pipette\nOpentrons 20\u00b5L Tip Racks\nOpentrons 300\u00b5L Tip Racks\nNEST 12-Well Reservoir, 15mL\nBio-Rad 96-Well PCR Plate, 200\u00b5L\nZymo Quick-DNA HMW MagBead Kit\nReagents for Labelling\nSamples\n\n\n\nDeck Layout\n\nSlot 1: Opentrons Temperatue Module, GEN2 with Bio-Rad 96-Well PCR Plate, 200\u00b5L on 96-Well Aluminum Block, containing samples in columns 1-4\n\nSlot 2: Bio-Rad 96-Well PCR Plate, 200\u00b5L (Labelling Plate)\nColumn 1: MTC22\nColumn 3: CSB\nColumn 5: M.Taql\nColumn 7: Proteinase K\n\nSlot 3: Opentrons 20\u00b5L Tip Racks (for Labelling)\n\nSlot 4: Opentrons Magnetic Module, GEN2 with Bio-Rad 96-Well PCR Plate, 200\u00b5L (empty)\n\nSlot 5: NEST 12-Well Reservoir, 15mL\nColumn 1: MilliQ Water\nColumn 2: MagBeads\nColumn 3: MagBinding Buffer\nColumn 4: Wash Buffer 1\nColumn 5: Wash Buffer 2\nColumn 6: Elution Buffer\n\nSlot 6: Opentrons 20\u00b5L Tip Racks (for Labelling)\n\nSlot 7: Opentrons 300\u00b5L Tip Racks (for Purification)\n\nSlot 8: Opentrons 300\u00b5L Tip Racks (for Purification)\n\nSlot 10: Opentrons 300\u00b5L Tip Racks (for Purification)\n\nSlot 11: Opentrons 20\u00b5L Tip Racks (for Purification)\n\nUsing the customizations field (below), set up your protocol.\n* P20-Multi Mount: Specify which mount the Opentrons P20 8-Channel Pipette is attached to.\n* P300-Multi Mount: Specify which mount the Opentrons P3000 8-Channel Pipette is attached to.\n* Labelling Step: Specify whether or not to run the labelling portion.\n* Purification Step: Specify whether or not to run the purification portion.", + "description": "This protocol automates the Zymo Quick-DNA HMW MagBead Kit with an additional labelling step that takes place before the purification.\n\nThe parameter section below gives you the ability to select either the Labelling portion of the protocol or the Purification portion of the protocol (you can select both). During the labelling portion, MilliQ Water, CSB, M.Taql, MTC22, and Proteinase K are added to the samples and the samples incubate while on the Temperature Module. During the purification portion, the samples are purified using the Zymo MagBead Kit in conjunction with Opentrons Magnetic Module.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nOpentrons Temperatue Module, GEN2\nOpentrons Magnetic Module, GEN2\nOpentrons P20 8-Channel Pipette\nOpentrons P300 8-Channel Pipette\nOpentrons 20\u00b5L Tip Racks\nOpentrons 300\u00b5L Tip Racks\nNEST 12-Well Reservoir, 15mL\nBio-Rad 96-Well PCR Plate, 200\u00b5L\nZymo Quick-DNA HMW MagBead Kit\nReagents for Labelling\nSamples\n\n\n\nDeck Layout\n\nSlot 1: Opentrons Temperatue Module, GEN2 with Bio-Rad 96-Well PCR Plate, 200\u00b5L on 96-Well Aluminum Block, containing samples in columns 1-4\n\nSlot 2: Bio-Rad 96-Well PCR Plate, 200\u00b5L (Labelling Plate)\nColumn 1: MTC22\nColumn 3: CSB\nColumn 5: M.Taql\nColumn 7: Proteinase K\n\nSlot 3: Opentrons 20\u00b5L Tip Racks (for Labelling)\n\nSlot 4: Opentrons Magnetic Module, GEN2 with Bio-Rad 96-Well PCR Plate, 200\u00b5L (empty)\n\nSlot 5: NEST 12-Well Reservoir, 15mL\nColumn 1: MilliQ Water\nColumn 2: MagBeads\nColumn 3: MagBinding Buffer\nColumn 4: Wash Buffer 1\nColumn 5: Wash Buffer 2\nColumn 6: Elution Buffer\n\nSlot 6: Opentrons 20\u00b5L Tip Racks (for Labelling)\n\nSlot 7: Opentrons 300\u00b5L Tip Racks (for Purification)\n\nSlot 8: Opentrons 300\u00b5L Tip Racks (for Purification)\n\nSlot 10: Opentrons 300\u00b5L Tip Racks (for Purification)\n\nSlot 11: Opentrons 20\u00b5L Tip Racks (for Purification)\n\nUsing the customizations field (below), set up your protocol.\n P20-Multi Mount: Specify which mount the Opentrons P20 8-Channel Pipette is attached to.\n P300-Multi Mount: Specify which mount the Opentrons P3000 8-Channel Pipette is attached to.\n Labelling Step: Specify whether or not to run the labelling portion.\n Purification Step: Specify whether or not to run the purification portion.", "internal": "71381b", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7363e4/README.json b/protoBuilds/7363e4/README.json index 49fd9192a..7ddef927d 100644 --- a/protoBuilds/7363e4/README.json +++ b/protoBuilds/7363e4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nOpentrons p1000 tips (Deck Slot 11)\n15 or 40-well custom rack or empty slot as specified in pulldown lists (Deck Slots 8-9)\nopentrons_24_tuberack_nest_1.5ml_snapcap or opentrons_24_tuberack_nest_2ml_snapcap as specified with pulldown list (up to 8 racks as displayed in OT app with deck slot fill order 10, 7, 4, 5, 6, 1, 2, 3)\n", - "description": "This protocol uses a p1000 single channel pipette to divide up to forty eight 3 mL clinical samples each into four aliquots with aliquot volumes of 1 mL, 0.5 mL, 0.5 mL and 1 mL.\nLinks:\n* Custom Aliquoting\n* Custom Pooling", + "description": "This protocol uses a p1000 single channel pipette to divide up to forty eight 3 mL clinical samples each into four aliquots with aliquot volumes of 1 mL, 0.5 mL, 0.5 mL and 1 mL.\nLinks:\n Custom Aliquoting\n Custom Pooling", "internal": "7363e4", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/743f54/README.json b/protoBuilds/743f54/README.json index b5c155b1b..6d16bdf7b 100644 --- a/protoBuilds/743f54/README.json +++ b/protoBuilds/743f54/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates preparation of plates that will be used in the Magnetic Particle Processing protocol on the KingFisher Flex.\nThis protocol is still a work in progress and will be updated.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples to be run (1-96).\n* Pipette Mount: Select which mount the P300 Single-Channel Pipette (GEN2) is attached to.\n", + "description": "This protocol automates preparation of plates that will be used in the Magnetic Particle Processing protocol on the KingFisher Flex.\nThis protocol is still a work in progress and will be updated.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples to be run (1-96).\n Pipette Mount: Select which mount the P300 Single-Channel Pipette (GEN2) is attached to.\n", "internal": "743f54", "labware": "\nOpentrons 200\u00b5L Filter Tips\nOpentrons 4-in-1 Tube Rack (with 24 Well Insert)\nReservoirs for Wash Buffers (like the NEST 1-Well Reservoir, 195mL)\nReservoir for Elution Buffer (like the NEST 12-Well Reservoir, 15mL)\n1.5mL Mictrocentrifuge Tube\nKingFisher 96-Deepwell Plate\nKingFisher 96-Well Microplate\n", "markdown": { diff --git a/protoBuilds/74750e/README.json b/protoBuilds/74750e/README.json index 8e7490b86..343deaac9 100644 --- a/protoBuilds/74750e/README.json +++ b/protoBuilds/74750e/README.json @@ -5,7 +5,7 @@ "Serial Dilution" ] }, - "description": "This protocol performs a simple serial dilution (factor 10) within each well plate for a specified number of well plates. 100ul of solution is mixed 12 times in each column before 20ul is transferred to the following column, with the mix-transfer iteration repeated up to the specified number of columns. New tips are granted between each well plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nCorning 96 Well Plate 360 \u00b5L Flat\n\n\n\nSlot 1: 96 Tip Rack 300 \u00b5L\nSlot 2 - (up to 11): Corning 96 Well Plate 360 \u00b5L Flat\nP300-Multi Mount: Left\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Columns: Specify number of columns with solution in each well plate.\n* Number of Plates: Specify number of plates for serial dilution.", + "description": "This protocol performs a simple serial dilution (factor 10) within each well plate for a specified number of well plates. 100ul of solution is mixed 12 times in each column before 20ul is transferred to the following column, with the mix-transfer iteration repeated up to the specified number of columns. New tips are granted between each well plate.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Multi-Channel Pipette\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nCorning 96 Well Plate 360 \u00b5L Flat\n\n\n\nSlot 1: 96 Tip Rack 300 \u00b5L\nSlot 2 - (up to 11): Corning 96 Well Plate 360 \u00b5L Flat\nP300-Multi Mount: Left\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Columns: Specify number of columns with solution in each well plate.\n Number of Plates: Specify number of plates for serial dilution.", "internal": "74750e", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/747d99-assay-1/README.json b/protoBuilds/747d99-assay-1/README.json index 5244cb1da..4589405f3 100644 --- a/protoBuilds/747d99-assay-1/README.json +++ b/protoBuilds/747d99-assay-1/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This protocol is a full COVID-19 diagnostic workflow up to RNA amplification. Samples are loaded in 15ml tubes and transferred to 1.5ml tubes for lysis and temperature incubations on an Opentrons temperature module. The samples are then transferred to a deepwell plate mounted on an Opentrons magnetic module for a 1-wash magnetic bead-based RNA extraction.\nExplanation of protocol parameters below:\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module GEN2\nOpentrons temperature module GEN2\nNEST 12 Well Reservoir 15 mL\nUSA Scientific PlateOne 96 Deepwell Plate 2mL\nOpentrons 96 Filter Tip Rack 200 and 1000 \u00b5L\nOpentrons P300-Multi GEN2 and P1000-Single GEN2 electronic pipettes\n\n\n \n \nReservoir (slot 2):\n* channel 1: lysis and hybridization buffer (HB1)\n* channel 2: magnetic beads\n* channel 4: wash buffer\n* channel 5: master mix\n* channel 12: liquid waste (loaded empty)", + "description": "This protocol is a full COVID-19 diagnostic workflow up to RNA amplification. Samples are loaded in 15ml tubes and transferred to 1.5ml tubes for lysis and temperature incubations on an Opentrons temperature module. The samples are then transferred to a deepwell plate mounted on an Opentrons magnetic module for a 1-wash magnetic bead-based RNA extraction.\nExplanation of protocol parameters below:\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module GEN2\nOpentrons temperature module GEN2\nNEST 12 Well Reservoir 15 mL\nUSA Scientific PlateOne 96 Deepwell Plate 2mL\nOpentrons 96 Filter Tip Rack 200 and 1000 \u00b5L\nOpentrons P300-Multi GEN2 and P1000-Single GEN2 electronic pipettes\n\n\n \n \nReservoir (slot 2):\n channel 1: lysis and hybridization buffer (HB1)\n channel 2: magnetic beads\n channel 4: wash buffer\n channel 5: master mix\n* channel 12: liquid waste (loaded empty)", "internal": "747d99", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/747d99-assay-2/README.json b/protoBuilds/747d99-assay-2/README.json index 46ec08180..2e50b6a9d 100644 --- a/protoBuilds/747d99-assay-2/README.json +++ b/protoBuilds/747d99-assay-2/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This protocol is a full COVID-19 diagnostic workflow up to RNA amplification. Samples are loaded in 15ml tubes and transferred to a 96-wellplate for lysis and temperature incubations on an Opentrons temperature module. The samples are then transferred to a deepwell plate mounted on an Opentrons magnetic module for a 1-wash magnetic bead-based RNA extraction.\nExplanation of protocol parameters below:\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module GEN2\nOpentrons temperature module GEN2\nNEST 12 Well Reservoir 15 mL\nUSA Scientific PlateOne 96 Deepwell Plate 2mL\nBio-Rad 96 Well Plate 350 \u00b5L PCR\nOpentrons 96 Filter Tip Rack 200 and 1000 \u00b5L\nOpentrons P300-Multi GEN2 and P1000-Single GEN2 electronic pipettes\n\n\n \n \nReservoir (slot 2):\n* channel 2: magnetic beads\n* channel 4: wash buffer\n* channel 5: master mix\n* channel 12: liquid waste (loaded empty)", + "description": "This protocol is a full COVID-19 diagnostic workflow up to RNA amplification. Samples are loaded in 15ml tubes and transferred to a 96-wellplate for lysis and temperature incubations on an Opentrons temperature module. The samples are then transferred to a deepwell plate mounted on an Opentrons magnetic module for a 1-wash magnetic bead-based RNA extraction.\nExplanation of protocol parameters below:\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module GEN2\nOpentrons temperature module GEN2\nNEST 12 Well Reservoir 15 mL\nUSA Scientific PlateOne 96 Deepwell Plate 2mL\nBio-Rad 96 Well Plate 350 \u00b5L PCR\nOpentrons 96 Filter Tip Rack 200 and 1000 \u00b5L\nOpentrons P300-Multi GEN2 and P1000-Single GEN2 electronic pipettes\n\n\n \n \nReservoir (slot 2):\n channel 2: magnetic beads\n channel 4: wash buffer\n channel 5: master mix\n channel 12: liquid waste (loaded empty)", "internal": "747d99", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/74841a-2/README.json b/protoBuilds/74841a-2/README.json index 1a07e6166..104e47f80 100644 --- a/protoBuilds/74841a-2/README.json +++ b/protoBuilds/74841a-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "Links:\n* Part 1\n* Part 2\nThis is Part 2/2 of the Swift Normalase Amplicon Panels (SNAP) Size Selection and Cleanup protocol.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n", + "description": "Links:\n Part 1\n Part 2\nThis is Part 2/2 of the Swift Normalase Amplicon Panels (SNAP) Size Selection and Cleanup protocol.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n", "internal": "74841a", "labware": "\nUSA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL or equivalent for waste\nBio-Rad 96 Well Plate 200 \u00b5L PCR Full Skirt\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { @@ -30,7 +30,7 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nOpentrons P300 8-Channel Electronic Pipette (GEN2)\nOpentrons P20 8-Channel Electronic Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "Reagent Reservoir (slot 5; volumes for 96-sample run):\n* channel 5: PEG, 3120\u00b5l\n* channel 6: EtOH, 17280\u00b5l\n* channel 7: EtOH, 17280\u00b5l\n* channel 8: POST-PCR TE buffer, 1920\u00b5l", + "reagent-setup": "Reagent Reservoir (slot 5; volumes for 96-sample run):\n channel 5: PEG, 3120\u00b5l\n channel 6: EtOH, 17280\u00b5l\n channel 7: EtOH, 17280\u00b5l\n channel 8: POST-PCR TE buffer, 1920\u00b5l", "reagents": [ "Swift Normalase Amplicon Panels (SNAP)" ], diff --git a/protoBuilds/74841a/README.json b/protoBuilds/74841a/README.json index ecd7984a1..307495148 100644 --- a/protoBuilds/74841a/README.json +++ b/protoBuilds/74841a/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "Links:\n* Part 1\n* Part 2\nThis is Part 1/2 of the Swift Normalase Amplicon Panels (SNAP) Size Selection and Cleanup protocol.\nLysed samples should be loaded on the magnetic module in a Bio-Rad 96-well PCR plate.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n", + "description": "Links:\n Part 1\n Part 2\nThis is Part 1/2 of the Swift Normalase Amplicon Panels (SNAP) Size Selection and Cleanup protocol.\nLysed samples should be loaded on the magnetic module in a Bio-Rad 96-well PCR plate.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n", "internal": "74841a", "labware": "\nUSA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL or equivalent for waste\nBio-Rad 96 Well Plate 200 \u00b5L PCR Full Skirt\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nOpentrons 96 Filter Tip Rack 20 \u00b5L\n", "markdown": { @@ -30,7 +30,7 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nOpentrons P300 8-Channel Electronic Pipette (GEN2)\nOpentrons P20 8-Channel Electronic Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "Reagent Reservoir (slot 5; volumes for 96-sample run):\n* channel 1: magnetic beads, 2880\u00b5l\n* channel 2: EtOH, 17280\u00b5l\n* channel 3: EtOH, 17280\u00b5l\n* channel 4: POST-PCR TE buffer, 1670.4\u00b5l", + "reagent-setup": "Reagent Reservoir (slot 5; volumes for 96-sample run):\n channel 1: magnetic beads, 2880\u00b5l\n channel 2: EtOH, 17280\u00b5l\n channel 3: EtOH, 17280\u00b5l\n channel 4: POST-PCR TE buffer, 1670.4\u00b5l", "reagents": [ "Swift Normalase Amplicon Panels (SNAP)" ], diff --git a/protoBuilds/7663a6/README.json b/protoBuilds/7663a6/README.json index c2b6e0114..4e36b54bd 100644 --- a/protoBuilds/7663a6/README.json +++ b/protoBuilds/7663a6/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nDeck Setup running 10 columns. Mastermix is held in A1 of the tube rack on Slot 3.\n\n\n", - "description": "This protocol preps a 96 well plate by column with mastermix and sample. Mastermix is held in an Opentrons 24-tube aluminum block without the temperature module. The aluminum block is placed in the freezer prior to running to keep mastermix cool.\nExplanation of complex parameters below:\n* Number of Columns: Input number of sample columns for this run.\n* Source Plate Starting Column: Specify the source plate starting column for samples.\n* Destination Plate Starting Column: Specify the destination plate starting column.\n* Sample Volume (ul): Specify sample volume in ul.\n* Mastermix Volume (ul): Specify mastermix volume in ul.\n* Source Aspiration Height (Plate): Specify aspiration height (in mm) from the bottom of the well in the sample plate.\n* Source Aspiration Height (Tube): Specify aspiration height (in mm) from the bottom of the tube in the mastermix tube.\n* Source Aspiration Flow Rate Sample (ul/sec): Specify the aspiration flow rate for sample.\n* Delay After Aspiration Mastermix (seconds): Specify the delay after aspirating mastermix in the tube. This may be helpful with viscous liquids, allowing the pipette time to achieve the full volume before moving on.\n* Source Aspiration Flow Rate Mastermix (ul/sec): Specify the aspiration flow rate for mastermix.\n* Dispense Height (from bottom): Specify dispense height (in mm) from the bottom of the well in the destination plate.\n* Dispense Flow Rate Sample: Specify the dispense flow rate of sample into destination plate.\n* Dispense Flow Rate Mastermix: Specify the dispense flow rate of mastermix into destination plate.\n* Mix Repetitions: Specify number of mix steps.\n* Touch Tip?: Specify whether to include touch tip in this run.\n* Blowout?: Specify whether to include blow out in this run.\n* P20 Single Mount: Specify left or right mount for the P20 single.\n* P20 Multi Mount: Specify left or right mount for the P20 multi.\n", + "description": "This protocol preps a 96 well plate by column with mastermix and sample. Mastermix is held in an Opentrons 24-tube aluminum block without the temperature module. The aluminum block is placed in the freezer prior to running to keep mastermix cool.\nExplanation of complex parameters below:\n Number of Columns: Input number of sample columns for this run.\n Source Plate Starting Column: Specify the source plate starting column for samples.\n Destination Plate Starting Column: Specify the destination plate starting column.\n Sample Volume (ul): Specify sample volume in ul.\n Mastermix Volume (ul): Specify mastermix volume in ul.\n Source Aspiration Height (Plate): Specify aspiration height (in mm) from the bottom of the well in the sample plate.\n Source Aspiration Height (Tube): Specify aspiration height (in mm) from the bottom of the tube in the mastermix tube.\n Source Aspiration Flow Rate Sample (ul/sec): Specify the aspiration flow rate for sample.\n Delay After Aspiration Mastermix (seconds): Specify the delay after aspirating mastermix in the tube. This may be helpful with viscous liquids, allowing the pipette time to achieve the full volume before moving on.\n Source Aspiration Flow Rate Mastermix (ul/sec): Specify the aspiration flow rate for mastermix.\n Dispense Height (from bottom): Specify dispense height (in mm) from the bottom of the well in the destination plate.\n Dispense Flow Rate Sample: Specify the dispense flow rate of sample into destination plate.\n Dispense Flow Rate Mastermix: Specify the dispense flow rate of mastermix into destination plate.\n Mix Repetitions: Specify number of mix steps.\n Touch Tip?: Specify whether to include touch tip in this run.\n Blowout?: Specify whether to include blow out in this run.\n P20 Single Mount: Specify left or right mount for the P20 single.\n P20 Multi Mount: Specify left or right mount for the P20 multi.\n", "internal": "7663a6", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\n", "markdown": { diff --git a/protoBuilds/76ab0e/README.json b/protoBuilds/76ab0e/README.json index 4354d1df8..80cfa7cee 100644 --- a/protoBuilds/76ab0e/README.json +++ b/protoBuilds/76ab0e/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol is based on the ML_normalization protocol and it performs a custom sample normalization from a source PCR plate to a second PCR plate, diluting with diluent (e.g. buffer or water) from a reservoir. Sample and diluent volumes are specified via .csv file in the following format, including the header line (empty lines ignored):\nsource plate well,destination plate well,volume sample (\u00b5l),volume diluent (\u00b5l)\nA1, A1, 2, 28\nDiluent is transferred first from the 12 well reservoir to the target plate wells as specified in the csv using the same pipette tip. After finishing, the pipette(s) drop their/its tip(s) and transfer samples to the target wells.\nThis protocol loads the sample and destination plate on 2nd generation temperature modules\nExplanation of parameters below:\n* input .csv file: Here, you should upload a .csv file formatted as described above.\n* P20 GEN2 mount: Choose whether to load the p20 in the right or left mount\n* P300 GEN2 mount: Choose whether to load the p300 in the right or left mount\n* Aspiration height from bottom of the plate wells [mm]: Offset to aspirate from the bottom of the source plate wells (in units of mm)\n* Dispensing height from bottom of the plate wells [mm]: Offset for dispenses from the bottom of the destination plate wells (in units of mm)\n* Aspiration height from bottom of the reservoir wells [mm]: Offset to aspirate from the bottom of the reservoir wells (in units of mm)\n* Flow rate multiplier: By setting this multiplier to a value 0 < x < 1 the rate of sample aspiration and dispensing will be slowed down. The default value is 0.5 resulting in aspiration at half of the regular speed.\n", + "description": "This protocol is based on the ML_normalization protocol and it performs a custom sample normalization from a source PCR plate to a second PCR plate, diluting with diluent (e.g. buffer or water) from a reservoir. Sample and diluent volumes are specified via .csv file in the following format, including the header line (empty lines ignored):\nsource plate well,destination plate well,volume sample (\u00b5l),volume diluent (\u00b5l)\nA1, A1, 2, 28\nDiluent is transferred first from the 12 well reservoir to the target plate wells as specified in the csv using the same pipette tip. After finishing, the pipette(s) drop their/its tip(s) and transfer samples to the target wells.\nThis protocol loads the sample and destination plate on 2nd generation temperature modules\nExplanation of parameters below:\n input .csv file: Here, you should upload a .csv file formatted as described above.\n P20 GEN2 mount: Choose whether to load the p20 in the right or left mount\n P300 GEN2 mount: Choose whether to load the p300 in the right or left mount\n Aspiration height from bottom of the plate wells [mm]: Offset to aspirate from the bottom of the source plate wells (in units of mm)\n Dispensing height from bottom of the plate wells [mm]: Offset for dispenses from the bottom of the destination plate wells (in units of mm)\n Aspiration height from bottom of the reservoir wells [mm]: Offset to aspirate from the bottom of the reservoir wells (in units of mm)\n* Flow rate multiplier: By setting this multiplier to a value 0 < x < 1 the rate of sample aspiration and dispensing will be slowed down. The default value is 0.5 resulting in aspiration at half of the regular speed.\n", "internal": "76ab0e", "labware": "\nAluminum Block Set\nBio-Rad 96 Well Plate 200 \u00b5L PCR\nNEST 12 well 15 mL reservoir\n", "markdown": { diff --git a/protoBuilds/76ba23-bisulfite_conversion/README.json b/protoBuilds/76ba23-bisulfite_conversion/README.json index 5291a6123..032c36b0d 100644 --- a/protoBuilds/76ba23-bisulfite_conversion/README.json +++ b/protoBuilds/76ba23-bisulfite_conversion/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slots 6 and 9)\n96 cell free DNA samples (\"nest_96_wellplate_100ul_pcr_full_skirt\" Deck slot 1)\npcr plate for CT conversion (\"biorad_96_wellplate_200ul_pcr\" Deck slot 2)\nreservoir for CT conv buffer, beads, water (\"nest_12_reservoir_15ml\" Deck slot 5)\nreservoir for wash (\"nest_1_reservoir_195ml\" Deck slot 5)\nreservoir for desulph buffer (\"nest_1_reservoir_195ml\" Deck slot 8)\npcr plate for eluate (\"nest_96_wellplate_100ul_pcr_full_skirt\" Deck slot 10)\nreservoir for waste (\"agilent_1_reservoir_290ml\" Deck slot 11)\n", - "description": "Part 2 of 5: Cell-free DNA (output from step 1) is chemically treated to convert unmethylated cytosine (C to T) in order to reveal patterns of methylated cytosine by DNA sequencing (methylated cytosine is protected and remains unchanged). This bisulfite conversion is followed by bead-clean up, elution, and transfer of the eluate to a fresh PCR plate.\nLinks:\n* Part 1: DNA Extraction\n* Part 2: Bisulfite Conversion\n* Part 3: PCR1\n* Part 4: PCR2\n* Part 5: Pooling\nWith this protocol, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 2 of the protocol: Bisulfite Conversion.\nThis step performs the bisulfite conversion and bead-clean up steps using the output samples from step 1 (DNA extraction).\nAfter the steps carried out in this protocol (part 2), proceed with part 3: PCR1.", + "description": "Part 2 of 5: Cell-free DNA (output from step 1) is chemically treated to convert unmethylated cytosine (C to T) in order to reveal patterns of methylated cytosine by DNA sequencing (methylated cytosine is protected and remains unchanged). This bisulfite conversion is followed by bead-clean up, elution, and transfer of the eluate to a fresh PCR plate.\nLinks:\n Part 1: DNA Extraction\n Part 2: Bisulfite Conversion\n Part 3: PCR1\n Part 4: PCR2\n* Part 5: Pooling\nWith this protocol, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 2 of the protocol: Bisulfite Conversion.\nThis step performs the bisulfite conversion and bead-clean up steps using the output samples from step 1 (DNA extraction).\nAfter the steps carried out in this protocol (part 2), proceed with part 3: PCR1.", "internal": "76ba23-bisulfite_conversion", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/76ba23-pcr1/README.json b/protoBuilds/76ba23-pcr1/README.json index 730485a92..5e1f9ff94 100644 --- a/protoBuilds/76ba23-pcr1/README.json +++ b/protoBuilds/76ba23-pcr1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slots 6, 9, 8, 11)\n96 samples from step 2 (\"nest_96_wellplate_100ul_pcr_full_skirt\" Deck slot 1)\npcr1 master mix (\"corning_96_wellplate_360ul_flat\" Deck slot 3)\ntrough for beads, water, waste (\"nest_12_reservoir_15ml\" Deck slot 5)\npcr plate (\"nest_96_wellplate_100ul_pcr_full_skirt\" Deck slot 2)\nreservoir for ethanol (\"nest_1_reservoir_195ml\" Deck slot 7)\n", - "description": "Part 3 of 5: Bisulfite converted DNA (output from step 2) is set up for a PCR amplification step. For plasma samples (but not saliva) the protocol includes post-PCR clean up steps.\nLinks:\n* Part 1: DNA Extraction\n* Part 2: Bisulfite Conversion\n* Part 3: PCR1\n* Part 4: PCR2\n* Part 5: Pooling\nWith this work flow, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 3 of the work flow: Bisulfite Conversion.\nThis step performs set up for PCR amplification (with additional post-PCR clean up steps for plasma samples only) using the output samples from step 2 (Bisulfite Conversion).\nAfter the steps carried out in this protocol (part 3), proceed with part 4: PCR2.", + "description": "Part 3 of 5: Bisulfite converted DNA (output from step 2) is set up for a PCR amplification step. For plasma samples (but not saliva) the protocol includes post-PCR clean up steps.\nLinks:\n Part 1: DNA Extraction\n Part 2: Bisulfite Conversion\n Part 3: PCR1\n Part 4: PCR2\n* Part 5: Pooling\nWith this work flow, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 3 of the work flow: Bisulfite Conversion.\nThis step performs set up for PCR amplification (with additional post-PCR clean up steps for plasma samples only) using the output samples from step 2 (Bisulfite Conversion).\nAfter the steps carried out in this protocol (part 3), proceed with part 4: PCR2.", "internal": "76ba23-pcr1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/76ba23-pcr2/README.json b/protoBuilds/76ba23-pcr2/README.json index a27e11cbf..ed0175613 100644 --- a/protoBuilds/76ba23-pcr2/README.json +++ b/protoBuilds/76ba23-pcr2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons p10 tips (Deck Slots 8, 11, 7, 10)\n1 or 2 plates each with 96 samples (output from PCR 1) (Deck slots 1 and 4)\npcr2 mix (\"corning_96_wellplate_360ul_flat\" Deck slot 9)\n1 or 2 plates each with 96 unique barcoded primers (Deck slots 2 and 5)\n1 or 2 pcr plates for PCR 2 (Deck slots 3 and 6)\n", - "description": "Part 4 of 5: PCR 1 product (output from step 2) is set up for a second PCR step featuring a unique forward primer for each plate (the forward primer is in the pcr2 mix, so different mixes should be used for each plate) and a unique, barcoded reverse primer for each well (there are two plates of unique barcodes for a total of 192).\nLinks:\n* Part 1: DNA Extraction\n* Part 2: Bisulfite Conversion\n* Part 3: PCR1\n* Part 4: PCR2\n* Part 5: Pooling\nWith this work flow, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 4 of the work flow: PCR 2.\nThis step performs set up for a second PCR amplification using the output samples from PCR 1 as the starting template. A unique forward primer is used for each plate (so a different tube of pcr2 mix will be used for each plate). A unique reverse primer will be used for each well. There are 192 unique, barcoded reverse primers between the two barcode plates.\nAfter the steps carried out in this protocol (part 4), proceed with part 5: pooling.", + "description": "Part 4 of 5: PCR 1 product (output from step 2) is set up for a second PCR step featuring a unique forward primer for each plate (the forward primer is in the pcr2 mix, so different mixes should be used for each plate) and a unique, barcoded reverse primer for each well (there are two plates of unique barcodes for a total of 192).\nLinks:\n Part 1: DNA Extraction\n Part 2: Bisulfite Conversion\n Part 3: PCR1\n Part 4: PCR2\n* Part 5: Pooling\nWith this work flow, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 4 of the work flow: PCR 2.\nThis step performs set up for a second PCR amplification using the output samples from PCR 1 as the starting template. A unique forward primer is used for each plate (so a different tube of pcr2 mix will be used for each plate). A unique reverse primer will be used for each well. There are 192 unique, barcoded reverse primers between the two barcode plates.\nAfter the steps carried out in this protocol (part 4), proceed with part 5: pooling.", "internal": "76ba23-pcr2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/76ba23-pooling/README.json b/protoBuilds/76ba23-pooling/README.json index 1628f93b5..477dbd772 100644 --- a/protoBuilds/76ba23-pooling/README.json +++ b/protoBuilds/76ba23-pooling/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slot 3)\nOpentrons p10 tips (Deck Slots 8, 7)\n1 or 2 pcr plates PCR 2 product from previous step (Deck slots 2 and 5)\ntube rack for pools (Deck Slot 1)\ndeep well plate on Magnetic Module ('usascientific_96_wellplate_2.4ml_deep') with pool_1_clean_up (pool 1 temporary dispense location and for clean up steps), pool_2_clean_up (pool 2 temporary dispense location and for clean up steps), beads, etoh, water in 'A1', 'A2', 'A3', 'A4', 'A5'\n", - "description": "Part 5 of 5: 5 ul aliquots of PCR 2 product (output from step 4) are combined to form a single pool for each plate followed by bead clean up and transfer to a fresh tube.\nLinks:\n* Part 1: DNA Extraction\n* Part 2: Bisulfite Conversion\n* Part 3: PCR1\n* Part 4: PCR2\n* Part 5: Pooling\nWith this work flow, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 5 of the work flow: Pooling.\nThis step combines 5 ul aliquots of 96 post-PCR 2 samples into a single pool for either one or two post-PCR 2 plates. This step is followed by a bead clean up and transfer of the finished pools to clean tubes.", + "description": "Part 5 of 5: 5 ul aliquots of PCR 2 product (output from step 4) are combined to form a single pool for each plate followed by bead clean up and transfer to a fresh tube.\nLinks:\n Part 1: DNA Extraction\n Part 2: Bisulfite Conversion\n Part 3: PCR1\n Part 4: PCR2\n* Part 5: Pooling\nWith this work flow, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 5 of the work flow: Pooling.\nThis step combines 5 ul aliquots of 96 post-PCR 2 samples into a single pool for either one or two post-PCR 2 plates. This step is followed by a bead clean up and transfer of the finished pools to clean tubes.", "internal": "76ba23-pooling", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/76ba23/README.json b/protoBuilds/76ba23/README.json index d7da881b0..370e975e8 100644 --- a/protoBuilds/76ba23/README.json +++ b/protoBuilds/76ba23/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slots 6 and 9)\n96 patient samples (\"usascientific_96_wellplate_2.4ml_deep\" Deck slot 1)\nDNA extraction plate (\"usascientific_96_wellplate_2.4ml_deep\" Deck slot 2)\n(if sample volume >= 1 mL) duplicate DNA extraction plate (Deck slot 5)\nreservoir for bead premix, wash, ethanol (\"nest_1_reservoir_195ml\" Deck slot 3)\npcr plate for eluate (\"nest_96_wellplate_100ul_pcr_full_skirt\" Deck slot 10)\nreservoir for waste (\"nest_1_reservoir_195ml\" Deck slot 11)\n", - "description": "Part 1 of 5: Extraction and clean-up of cell-free DNA from 96 plasma or saliva patient specimens.\nLinks:\n* Part 1: DNA Extraction\n* Part 2: Bisulfite Conversion\n* Part 3: PCR1\n* Part 4: PCR2\n* Part 5: Pooling\nWith this protocol, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 1 of the protocol: DNA Extraction.\nThis step performs the extraction and bead-clean up of 96 patient samples (plasma or saliva) listed in the sample manifest and follows the HKG SOP described above. A current sample manifest can be uploaded and integrated into this protocol by using the \"Uploaded CSV Copy of Sample Manifest\" parameter below. The OT-2 will read the sample type and sample volume from the uploaded manifest and then set up and perform the experimental steps accordingly.\nAfter the steps carried out in this protocol (part 1), proceed with part 2: Bisulfite Conversion.", + "description": "Part 1 of 5: Extraction and clean-up of cell-free DNA from 96 plasma or saliva patient specimens.\nLinks:\n Part 1: DNA Extraction\n Part 2: Bisulfite Conversion\n Part 3: PCR1\n Part 4: PCR2\n* Part 5: Pooling\nWith this protocol, your robot will use reagents from the Zymoresearch EZ DNA Methylation-Gold Kit Zymoresearch EZ DNA Methylation-Gold Kit to perform the custom steps (DNA extraction, Bisulfite Conversion, PCR1, PCR2, Pooling) detailed in the HKG SOP.HKG SOP.\nThis is part 1 of the protocol: DNA Extraction.\nThis step performs the extraction and bead-clean up of 96 patient samples (plasma or saliva) listed in the sample manifest and follows the HKG SOP described above. A current sample manifest can be uploaded and integrated into this protocol by using the \"Uploaded CSV Copy of Sample Manifest\" parameter below. The OT-2 will read the sample type and sample volume from the uploaded manifest and then set up and perform the experimental steps accordingly.\nAfter the steps carried out in this protocol (part 1), proceed with part 2: Bisulfite Conversion.", "internal": "76ba23", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/772041/README.json b/protoBuilds/772041/README.json index 329d5bc31..7d00edf11 100644 --- a/protoBuilds/772041/README.json +++ b/protoBuilds/772041/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol distributes PCR mastermix from a source NEST 12 well reservoir to a target Applied Biosystems Microamp optical 384 well 30 \u00b5L plate (or other PCR plate) with an 20 \u00b5L 8-channel pipette loaded in the left mount. The user can choose how many wells to transfer to (rounding up to the nearest number of columns) as well as how much volume to add to each well. The user can also choose whether they want to reuse tips, or pick up new tips for each transfer.\nExplanation of parameters below:\n* Number of wells to distribute mastermix to: How many wells to transfer mastermix to on the target plate. This will be rounded up to the nearest number of full columns.\n* Volume of mastermix: Volume of mastermix to add to each well (\u00b5L)\n* Reuse tips?: Yes: Reuse tips when distributing the mastermix. No: Drop the tips after each distribution, and pick up new tips before each aspiration.\n* Destination plate: What type of plate to distribute mastermix to\n", + "description": "This protocol distributes PCR mastermix from a source NEST 12 well reservoir to a target Applied Biosystems Microamp optical 384 well 30 \u00b5L plate (or other PCR plate) with an 20 \u00b5L 8-channel pipette loaded in the left mount. The user can choose how many wells to transfer to (rounding up to the nearest number of columns) as well as how much volume to add to each well. The user can also choose whether they want to reuse tips, or pick up new tips for each transfer.\nExplanation of parameters below:\n Number of wells to distribute mastermix to: How many wells to transfer mastermix to on the target plate. This will be rounded up to the nearest number of full columns.\n Volume of mastermix: Volume of mastermix to add to each well (\u00b5L)\n Reuse tips?: Yes: Reuse tips when distributing the mastermix. No: Drop the tips after each distribution, and pick up new tips before each aspiration.\n Destination plate: What type of plate to distribute mastermix to\n", "internal": "772041", "labware": "\nNEST 12-Well Reservoirs, 15 mL\nMicroAmp Optical 384-Well Reaction Plate with barcode\n20 \u00b5L filter tips\n", "markdown": { diff --git a/protoBuilds/7805de-part-2/README.json b/protoBuilds/7805de-part-2/README.json index c1bd84d2a..99df5953f 100644 --- a/protoBuilds/7805de-part-2/README.json +++ b/protoBuilds/7805de-part-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module and opentrons_96_aluminumblock_generic_pcr_strip_200ul (Deck Slot 3)\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slots 6 and 9)\nOpentrons p20 tips (Deck Slots 2 and 5)\nnest_12_reservoir_15ml (Deck Slot 1)\nnest_96_wellplate_100ul_pcr_full_skirt (Deck Slot 7)\n", - "description": "Part 2 of 4: First and second strand cDNA synthesis followed by bead clean up.\nLinks:\n* Part 1: RNA Isolation, Fragmentation and Priming\n* Part 2: cDNA Synthesis\n* Part 3: End Prep and Adapter Ligation\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 2 of the protocol: cDNA Synthesis.\nThis step performs first and second strand cDNA synthesis using the output plate from part 1. This protocol follows Section 1 of the NEB Instruction Manual.", + "description": "Part 2 of 4: First and second strand cDNA synthesis followed by bead clean up.\nLinks:\n Part 1: RNA Isolation, Fragmentation and Priming\n Part 2: cDNA Synthesis\n Part 3: End Prep and Adapter Ligation\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 2 of the protocol: cDNA Synthesis.\nThis step performs first and second strand cDNA synthesis using the output plate from part 1. This protocol follows Section 1 of the NEB Instruction Manual.", "internal": "7805de-part-2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7805de-part-3/README.json b/protoBuilds/7805de-part-3/README.json index c04750f47..bf44e759e 100644 --- a/protoBuilds/7805de-part-3/README.json +++ b/protoBuilds/7805de-part-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module and opentrons_96_aluminumblock_generic_pcr_strip_200ul (Deck Slot 3)\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slots 6 and 9)\nOpentrons p20 tips (Deck Slots 2 and 5)\nnest_12_reservoir_15ml (Deck Slot 1)\nnest_96_wellplate_100ul_pcr_full_skirt (Deck Slot 7)\n", - "description": "Part 3 of 4: Perform end-prep and adapter ligation steps with double-stranded cDNA output from part 2 followed by a bead clean up.\nLinks:\n* Part 1: RNA Isolation, Fragmentation and Priming\n* Part 2: cDNA Synthesis\n* Part 3: End Prep and Adapter Ligation\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 3 of the protocol: End Prep and Adapter Ligation.\nThis step prepares ends and ligates indexing primers to the cDNA in preparation for Illumina sequencing. This protocol follows Section 1 of the NEB Instruction Manual.", + "description": "Part 3 of 4: Perform end-prep and adapter ligation steps with double-stranded cDNA output from part 2 followed by a bead clean up.\nLinks:\n Part 1: RNA Isolation, Fragmentation and Priming\n Part 2: cDNA Synthesis\n Part 3: End Prep and Adapter Ligation\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 3 of the protocol: End Prep and Adapter Ligation.\nThis step prepares ends and ligates indexing primers to the cDNA in preparation for Illumina sequencing. This protocol follows Section 1 of the NEB Instruction Manual.", "internal": "7805de-part-3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7805de-part-4/README.json b/protoBuilds/7805de-part-4/README.json index 8f7300e90..265f42a18 100644 --- a/protoBuilds/7805de-part-4/README.json +++ b/protoBuilds/7805de-part-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module and opentrons_96_aluminumblock_generic_pcr_strip_200ul (Deck Slot 3)\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slots 6 and 9)\nOpentrons p20 tips (Deck Slots 2 and 5)\nnest_12_reservoir_15ml (Deck Slot 1)\nnest_96_wellplate_100ul_pcr_full_skirt (Deck Slot 7)\n", - "description": "Part 4 of 4: PCR enrichment and bead clean up of cDNA in preparation for Illumina sequencing.\nLinks:\n* Part 1: RNA Isolation, Fragmentation and Priming\n* Part 2: cDNA Synthesis\n* Part 3: End Prep and Adapter Ligation\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 4 of the protocol: PCR Enrichment.\nThis step amplifies end-prepped and adapter-ligated output from part 3 and then follows up with a bead clean up of the PCR product in preparation for Illumina sequencing. This protocol follows Section 1 of the NEB Instruction Manual.", + "description": "Part 4 of 4: PCR enrichment and bead clean up of cDNA in preparation for Illumina sequencing.\nLinks:\n Part 1: RNA Isolation, Fragmentation and Priming\n Part 2: cDNA Synthesis\n Part 3: End Prep and Adapter Ligation\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 4 of the protocol: PCR Enrichment.\nThis step amplifies end-prepped and adapter-ligated output from part 3 and then follows up with a bead clean up of the PCR product in preparation for Illumina sequencing. This protocol follows Section 1 of the NEB Instruction Manual.", "internal": "7805de-part-4", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7805de/README.json b/protoBuilds/7805de/README.json index f9042d484..ae4b3e33e 100644 --- a/protoBuilds/7805de/README.json +++ b/protoBuilds/7805de/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nOpentrons Temperature Module and opentrons_96_aluminumblock_generic_pcr_strip_200ul (Deck Slot 3)\nOpentrons Magnetic Module (Deck Slot 4)\nOpentrons p300 tips (Deck Slots 6 and 9)\nOpentrons p20 tips (Deck Slots 2 and 5)\nnest_12_reservoir_15ml (Deck Slot 1)\nnest_96_wellplate_100ul_pcr_full_skirt (Deck Slot 7)\n", - "description": "Part 1 of 4: Isolate poly(A) RNA from starting total RNA and perform fragmentation and priming in preparation for cDNA synthesis.\nLinks:\n* Part 1: RNA Isolation, Fragmentation and Priming\n* Part 2: cDNA Synthesis\n* Part 3: End Prep and Adapter Ligation\n* Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 1 of the protocol: RNA Isolation, Fragmentation and Priming.\nThis step isolates poly(A) RNA from up to 48 total RNA samples and then fragments and primes the RNA in preparation for cDNA synthesis (occurs in part 2). This protocol follows Section 1 of the NEB Instruction Manual.\nAfter the steps carried out in this protocol (part 1), it is best to immediately proceed with part 2: cDNA Synthesis.", + "description": "Part 1 of 4: Isolate poly(A) RNA from starting total RNA and perform fragmentation and priming in preparation for cDNA synthesis.\nLinks:\n Part 1: RNA Isolation, Fragmentation and Priming\n Part 2: cDNA Synthesis\n Part 3: End Prep and Adapter Ligation\n Part 4: PCR Enrichment\nWith this protocol, your robot can perform the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina protocol described by the NEB Instruction Manual.\nThis is part 1 of the protocol: RNA Isolation, Fragmentation and Priming.\nThis step isolates poly(A) RNA from up to 48 total RNA samples and then fragments and primes the RNA in preparation for cDNA synthesis (occurs in part 2). This protocol follows Section 1 of the NEB Instruction Manual.\nAfter the steps carried out in this protocol (part 1), it is best to immediately proceed with part 2: cDNA Synthesis.", "internal": "7805de", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef-part2/README.json b/protoBuilds/7855ef-part2/README.json index bc8cba63e..e847823a7 100644 --- a/protoBuilds/7855ef-part2/README.json +++ b/protoBuilds/7855ef-part2/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the second of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 2ul of Pre-ligation mix is distributed to each column of sample that was processed in Part 1 of the protocol.\nNote: This protocol was updated September 28th, 2022\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nApplied Biosystems 384 Well Plate\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 384).\n* P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 4 tip racks as in the original configuration of the deck.\nLabware Setup\nSlot 5: 384 well plate\nSlot 6: MMX Plate with Pre-ligation Mix in Column 3\nSlots 7, 8, 9, 10: Opentrons 20ul Tip Rack", + "description": "This protocol is the second of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 2ul of Pre-ligation mix is distributed to each column of sample that was processed in Part 1 of the protocol.\nNote: This protocol was updated September 28th, 2022\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nApplied Biosystems 384 Well Plate\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 384).\n P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 4 tip racks as in the original configuration of the deck.\nLabware Setup\nSlot 5: 384 well plate\nSlot 6: MMX Plate with Pre-ligation Mix in Column 3\nSlots 7, 8, 9, 10: Opentrons 20ul Tip Rack", "internal": "7855ef-part2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef-part3/README.json b/protoBuilds/7855ef-part3/README.json index c65839e72..fefe3364a 100644 --- a/protoBuilds/7855ef-part3/README.json +++ b/protoBuilds/7855ef-part3/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the third of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 1ul of IonCode Barcode Adapter is 1-1 transferred by well between the sample plate from Parts 1 & 2 and the Ion Code 96 well plate.\nNote: This protocol was updated November 22nd, 2022\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nApplied Biosystems 384 Well Plate\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 384).\n* P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nLabware Setup\nSlots 1, 2, 3: Ion Code Barcode plates (Custom 96 well Endura plate)\nSlot 5: 384 well plate\nSlot 7: MMX Plate with Barcode Reaction Mix in Column 4\nSlot 8, 9, 10, 11: Opentrons 20ul Tip Rack", + "description": "This protocol is the third of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 1ul of IonCode Barcode Adapter is 1-1 transferred by well between the sample plate from Parts 1 & 2 and the Ion Code 96 well plate.\nNote: This protocol was updated November 22nd, 2022\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nApplied Biosystems 384 Well Plate\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 384).\n P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nLabware Setup\nSlots 1, 2, 3: Ion Code Barcode plates (Custom 96 well Endura plate)\nSlot 5: 384 well plate\nSlot 7: MMX Plate with Barcode Reaction Mix in Column 4\nSlot 8, 9, 10, 11: Opentrons 20ul Tip Rack", "internal": "7855ef-part3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef-part4/README.json b/protoBuilds/7855ef-part4/README.json index 9e654fe93..7cc6b01a7 100644 --- a/protoBuilds/7855ef-part4/README.json +++ b/protoBuilds/7855ef-part4/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the fourth part of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. Samples in plate are pooled into 60ul pools on a well plate. After which, 45ul from each pool is pooled into a single column.\nNote: This protocol was updated on September 28th, 2022\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.7.0 or later)\nP20 8-Channel Pipette\nP300 8-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\nApplied Biosystems 384-Well Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 384).\n* P20 Mount: Specify which mount to load the P20 GEN2 pipette.\n* Tip Disposal: Set the pipette to return tips to the tip rack immediately after use or in the trash bin first.\nLabware Setup\nSlots 1: Pool Plate (Custom 96 well Endura Plate)\nSlot 5: Reaction Plate (Applied Biosystems 384-Well Plate)\nSlot 7, 8, 9, 10: Opentrons 20ul Filter Tip Rack(s)\nSlot 11: Opentrons 200ul Filter Tip Rack", + "description": "This protocol is the fourth part of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. Samples in plate are pooled into 60ul pools on a well plate. After which, 45ul from each pool is pooled into a single column.\nNote: This protocol was updated on September 28th, 2022\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.7.0 or later)\nP20 8-Channel Pipette\nP300 8-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\nApplied Biosystems 384-Well Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 384).\n P20 Mount: Specify which mount to load the P20 GEN2 pipette.\n* Tip Disposal: Set the pipette to return tips to the tip rack immediately after use or in the trash bin first.\nLabware Setup\nSlots 1: Pool Plate (Custom 96 well Endura Plate)\nSlot 5: Reaction Plate (Applied Biosystems 384-Well Plate)\nSlot 7, 8, 9, 10: Opentrons 20ul Filter Tip Rack(s)\nSlot 11: Opentrons 200ul Filter Tip Rack", "internal": "7855ef-part4", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef-plate-part2/README.json b/protoBuilds/7855ef-plate-part2/README.json index 1c8fc3bea..f6668f8b9 100644 --- a/protoBuilds/7855ef-plate-part2/README.json +++ b/protoBuilds/7855ef-plate-part2/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the second of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 2ul of Pre-ligation mix is distributed to each column of sample that was processed in Part 1 of the protocol.\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 288).\n* P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1, 2, 3: ThermoFisher Scientific (model AB0800) 96 well plate loaded with DNA sample. \nSlot 4, 5, 6: Custom 96 Well Endura Plate with reaction\nSlot 7: MMX Plate with Pre-ligation Mix in Column 2\nSlot 9, 10, 11: Opentrons 20ul Tip Rack", + "description": "This protocol is the second of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 2ul of Pre-ligation mix is distributed to each column of sample that was processed in Part 1 of the protocol.\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 288).\n P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1, 2, 3: ThermoFisher Scientific (model AB0800) 96 well plate loaded with DNA sample. \nSlot 4, 5, 6: Custom 96 Well Endura Plate with reaction\nSlot 7: MMX Plate with Pre-ligation Mix in Column 2\nSlot 9, 10, 11: Opentrons 20ul Tip Rack", "internal": "7855ef-96-plate-part2", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef-plate-part3/README.json b/protoBuilds/7855ef-plate-part3/README.json index e34d45dc0..6517cf1de 100644 --- a/protoBuilds/7855ef-plate-part3/README.json +++ b/protoBuilds/7855ef-plate-part3/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the third of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 1ul of IonCode Barcode Adapter is 1-1 transferred by well between the sample plate from Parts 1 & 2 and the Ion Code 96 well plate.\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 288).\n* P20 Multi GEN2 mount: Specify which mount to load the P20 Multi GEN2 pipette.\n* Overage percent for Barcode Reaction Mix in Slot 7, Column 3\nLabware Setup\nSlots 1, 2, 3: Ion Code Barcode plates (Custom 96 well Endura plate)\nSlot 4, 5, 6: Custom 96 Well Endura Plate with reaction\nSlot 7: MMX Plate with Barcode Reaction Mix in Column 3\nSlot 8, 9, 10: Opentrons 20ul Tip Rack", + "description": "This protocol is the third of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. 1ul of IonCode Barcode Adapter is 1-1 transferred by well between the sample plate from Parts 1 & 2 and the Ion Code 96 well plate.\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 288).\n P20 Multi GEN2 mount: Specify which mount to load the P20 Multi GEN2 pipette.\n* Overage percent for Barcode Reaction Mix in Slot 7, Column 3\nLabware Setup\nSlots 1, 2, 3: Ion Code Barcode plates (Custom 96 well Endura plate)\nSlot 4, 5, 6: Custom 96 Well Endura Plate with reaction\nSlot 7: MMX Plate with Barcode Reaction Mix in Column 3\nSlot 8, 9, 10: Opentrons 20ul Tip Rack", "internal": "7855ef-part3", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef-plate-part4/README.json b/protoBuilds/7855ef-plate-part4/README.json index 027026e98..3e1734fed 100644 --- a/protoBuilds/7855ef-plate-part4/README.json +++ b/protoBuilds/7855ef-plate-part4/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the fourth part of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. Samples in plate are pooled into 60ul pools on a well plate. After which, 45ul from each pool is transferred to the final processing plate.\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Single Channel Pipette\nP300 Single Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 288).\n* P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nLabware Setup\nSlots 1: Pool Plate 1 (Custom 96 well Endura Plate)\nSlot 2: Pool Plate 2 (Custom 96 well Endura Plate)\nSlot 4, 5, 6: Reaction Plates (Custom 96 well Endura Plate)\nSlot 8: Opentrons 200ul Tip Rack\nSlot 9, 10, 11: Opentrons 20ul Tip Rack", + "description": "This protocol is the fourth part of a four part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. Samples in plate are pooled into 60ul pools on a well plate. After which, 45ul from each pool is transferred to the final processing plate.\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Single Channel Pipette\nP300 Single Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nOpentrons 96 Filter Tip Rack 200 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 288).\n P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nLabware Setup\nSlots 1: Pool Plate 1 (Custom 96 well Endura Plate)\nSlot 2: Pool Plate 2 (Custom 96 well Endura Plate)\nSlot 4, 5, 6: Reaction Plates (Custom 96 well Endura Plate)\nSlot 8: Opentrons 200ul Tip Rack\nSlot 9, 10, 11: Opentrons 20ul Tip Rack", "internal": "7855ef-part4", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef-plate/README.json b/protoBuilds/7855ef-plate/README.json index c72da7330..71d00139f 100644 --- a/protoBuilds/7855ef-plate/README.json +++ b/protoBuilds/7855ef-plate/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the first of a 4 part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. The OT-2 will distribute 7ul of Amplification Mix to each well of 96 well plates up to the number of samples specified by the user. 3ul of DNA is then added to each well containing Ampflication Mix.\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\nNote about tips\nThe OT-2 will track tips from Part 1 to Part 4 of the protocol (e.g. tip leaves off in H11 at the end of protocol 1; first tip pick up will be from H12 in Part 2). When tips run out for any particular Part, the user will be prompted to replace all tip racks.\nUpdate (July 18, 2022): The custom touch tip has been adjusted\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\nNote About Sample Number\nPart 4 of this protocol will pool 5ul from wells until a 60ul pool is achieved (i.e. a full plate would have one pool per row). If there is less than a full plate loaded, the protocol will iterate through wells dependent on the sample number specified until 60ul is reached. Please consider the following examples:\n\n96 sample run (1 plate): 1 column of 60ul pools.\n144 sample run (1.5 plates): 1 column and 4 wells of 60ul pools.\n216 sample run (2.25 plates): 2 columns and 2 wells of 60ul pools.\n\nIt is thus critical to load samples that can be discretely divided by 12.\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 288).\n* P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1, 2, 3: ThermoFisher Scientific (model AB0800) 96 well plate loaded with DNA sample. \nSlot 4, 5, 6: Custom 96 Well Endura Plate (empty)\nSlot 7: MMX Plate with Amplification Mix in Column 1\nSlot 8, 9, 10, 11: Opentrons 20ul Tip Rack", + "description": "This protocol is the first of a 4 part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. The OT-2 will distribute 7ul of Amplification Mix to each well of 96 well plates up to the number of samples specified by the user. 3ul of DNA is then added to each well containing Ampflication Mix.\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\nNote about tips\nThe OT-2 will track tips from Part 1 to Part 4 of the protocol (e.g. tip leaves off in H11 at the end of protocol 1; first tip pick up will be from H12 in Part 2). When tips run out for any particular Part, the user will be prompted to replace all tip racks.\nUpdate (July 18, 2022): The custom touch tip has been adjusted\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\nNote About Sample Number\nPart 4 of this protocol will pool 5ul from wells until a 60ul pool is achieved (i.e. a full plate would have one pool per row). If there is less than a full plate loaded, the protocol will iterate through wells dependent on the sample number specified until 60ul is reached. Please consider the following examples:\n\n96 sample run (1 plate): 1 column of 60ul pools.\n144 sample run (1.5 plates): 1 column and 4 wells of 60ul pools.\n216 sample run (2.25 plates): 2 columns and 2 wells of 60ul pools.\n\nIt is thus critical to load samples that can be discretely divided by 12.\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 288).\n P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1, 2, 3: ThermoFisher Scientific (model AB0800) 96 well plate loaded with DNA sample. \nSlot 4, 5, 6: Custom 96 Well Endura Plate (empty)\nSlot 7: MMX Plate with Amplification Mix in Column 1\nSlot 8, 9, 10, 11: Opentrons 20ul Tip Rack", "internal": "7855ef", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7855ef/README.json b/protoBuilds/7855ef/README.json index 9b599b540..4acc61c55 100644 --- a/protoBuilds/7855ef/README.json +++ b/protoBuilds/7855ef/README.json @@ -5,7 +5,7 @@ "AgriSeq HTS Library Kit" ] }, - "description": "This protocol is the first of a 4 part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. The OT-2 will distribute 7ul of Amplification Mix to each well of a 384 well plate up to the number of samples specified by the user. 3ul of DNA is then added to each well containing Ampflication Mix.\nLinks:\n* Part 1: DNA Transfer\n* Part 2: Pre-Ligation\n* Part 3: Barcoding\n* Part 4: Pooling\nNote about tips\nThe OT-2 will track tips from Part 1 to Part 4 of the protocol (e.g. tip leaves off in H11 at the end of protocol 1; first tip pick up will be from H12 in Part 2). When tips run out for any particular Part, the user will be prompted to replace all tip racks.\nUpdate: This protocol was updated November 22nd, 2022\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.7.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nApplied Biosystems 384 Well Plate\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\nNote About Sample Number\nPart 4 of this protocol will pool 5ul from wells until a 60ul pool is achieved (i.e. a full plate would have one pool per row). If there is less than a full plate loaded, the protocol will iterate through wells dependent on the sample number specified until 60ul is reached. Please consider the following examples:\n\n96 sample run (1 plate): 1 column of 60ul pools.\n144 sample run (1.5 plates): 1 column and 4 wells of 60ul pools.\n216 sample run (2.25 plates): 2 columns and 2 wells of 60ul pools.\n\nIt is thus critical to load samples that can be discretely divided by 12.\n\n\nUsing the customization fields below, set up your protocol.\n* Number of Samples: Specify the number of samples to be processed in this run (max 384).\n* P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1, 2, 3, 4: ThermoFisher Scientific (model AB0800) 96 well plate loaded with DNA sample. \nSlot 5: 384 well plate\nSlot 6: MMX Plate with Amplification Mix in Column 1 and 2\nSlot 7, 8, 9, 10, 11: Opentrons 20ul Tip Rack", + "description": "This protocol is the first of a 4 part series for performing NGS library prep with the ThermoFisher Scientific AgriSeq kit. The OT-2 will distribute 7ul of Amplification Mix to each well of a 384 well plate up to the number of samples specified by the user. 3ul of DNA is then added to each well containing Ampflication Mix.\nLinks:\n Part 1: DNA Transfer\n Part 2: Pre-Ligation\n Part 3: Barcoding\n Part 4: Pooling\nNote about tips\nThe OT-2 will track tips from Part 1 to Part 4 of the protocol (e.g. tip leaves off in H11 at the end of protocol 1; first tip pick up will be from H12 in Part 2). When tips run out for any particular Part, the user will be prompted to replace all tip racks.\nUpdate: This protocol was updated November 22nd, 2022\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.7.0 or later)\nP20 Multi-Channel Pipette\nOpentrons 96 Filter Tip Rack 20 \u00b5L\nThermoFisher Scientific 96 Well Plate 200ul (AB-0800)\nThermoFisher Scientific 96 Well Plate 200ul (4483352)\nBioRad Hard-shell 96-well PCR Plate Skirted\nApplied Biosystems 384 Well Plate\nCustom 96 Well Endura Plate\n\nNote About Labware\nThe ThermoFisher 96 well plate (model 4483352) is to be mounted on top of the BioRad Hard-shell plate, making one plate with a moniker of \"Custom 96 Well Endura Plate\".\nNote About Sample Number\nPart 4 of this protocol will pool 5ul from wells until a 60ul pool is achieved (i.e. a full plate would have one pool per row). If there is less than a full plate loaded, the protocol will iterate through wells dependent on the sample number specified until 60ul is reached. Please consider the following examples:\n\n96 sample run (1 plate): 1 column of 60ul pools.\n144 sample run (1.5 plates): 1 column and 4 wells of 60ul pools.\n216 sample run (2.25 plates): 2 columns and 2 wells of 60ul pools.\n\nIt is thus critical to load samples that can be discretely divided by 12.\n\n\nUsing the customization fields below, set up your protocol.\n Number of Samples: Specify the number of samples to be processed in this run (max 384).\n P20 single GEN2 mount: Specify which mount to load the P20 single GEN2 pipette.\nNote about 20\u00b5L tip racks\nWhen prompted to replace the 20ul tip racks, be sure to re-load all 3 tip racks as in the original configuration of the deck.\nLabware Setup\nSlots 1, 2, 3, 4: ThermoFisher Scientific (model AB0800) 96 well plate loaded with DNA sample. \nSlot 5: 384 well plate\nSlot 6: MMX Plate with Amplification Mix in Column 1 and 2\nSlot 7, 8, 9, 10, 11: Opentrons 20ul Tip Rack", "internal": "7855ef", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/797dee-normalization/README.json b/protoBuilds/797dee-normalization/README.json index 316696e9b..bbb4df87d 100644 --- a/protoBuilds/797dee-normalization/README.json +++ b/protoBuilds/797dee-normalization/README.json @@ -5,7 +5,7 @@ "Normalization" ] }, - "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library prep. With this protocol, you can easily normalize the concentrations of samples in a 96 or 384 microwell plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nSamples in a compatible plate (96-well or 384-well)\nOpentrons 4-in-1 Tube Rack Set\nDiluent\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nCSV Format\nYour file must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). It should be formatted in \u201clandscape\u201d orientation, with the value corresponding to well A1 in the upper left-hand corner of the value list.\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, and so on.\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV from there.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).\nUsing the customization fields below, set up your protocol.\n* Volumes CSV: Upload the CSV (.csv) containing your diluent volumes.\n* Pipette Model: Select which pipette you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n* Plate Type: Select which (destination) plate you will use for this protocol.\n* Volume in 50ml: What is the starting volume of in your 50mL tube of diluent?\n* Filter Tips: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", + "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library prep. With this protocol, you can easily normalize the concentrations of samples in a 96 or 384 microwell plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nSamples in a compatible plate (96-well or 384-well)\nOpentrons 4-in-1 Tube Rack Set\nDiluent\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nCSV Format\nYour file must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). It should be formatted in \u201clandscape\u201d orientation, with the value corresponding to well A1 in the upper left-hand corner of the value list.\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, and so on.\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV from there.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).\nUsing the customization fields below, set up your protocol.\n Volumes CSV: Upload the CSV (.csv) containing your diluent volumes.\n Pipette Model: Select which pipette you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n Plate Type: Select which (destination) plate you will use for this protocol.\n Volume in 50ml: What is the starting volume of in your 50mL tube of diluent?\n Filter Tips: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", "internal": "normalization", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7a1ae8/README.json b/protoBuilds/7a1ae8/README.json index bb9903978..044a70050 100644 --- a/protoBuilds/7a1ae8/README.json +++ b/protoBuilds/7a1ae8/README.json @@ -5,7 +5,7 @@ "Zymo Kit" ] }, - "description": "This protocol performs a custom nucleic acid purification using the Zymobiomics Magbead kit. This protocol was updated from this to APIv2.\n\n\n\nNEST Deep Well Plate or similar\nOpentrons P300 Single-channel electronic pipette\nOpentrons P300 Multi-channel electronic pipette\nOpentrons 300ul tipracks\n\n\n\nSTARTING SETUP for 4x6 2ml screwcap tube aluminum block (slot 2):\n* tubes A1-D6: original samples (up to 24 samples aligned down columns and then across rows)\nMID-PROTOCOL SETUP for 4x6 2ml screwcap tube aluminum block (slot 2):\n* tubes A1-C1: molecular grade water tubes (1 tube for each 8 samples); note-- the user is prompted to replace these tubes midway through the protocol\n12-channel reagent reservoir (slot 4):\n* channel 1: mag binding buffer\n* channel 2: magnetic beads\n* channel 3: magwash 1\n* channels 4-5: magwash 2 (1 channel each for 2x washes)\nwaste reservoir (slot 11):\n* Note-- the reservoir is programmed as an Agilent 290ml single-channel reservoir, but the user can replace this with any reservoir of choice for containing the liquid waste throughout the protocol by calibrating to the top of the reservoir before the run.", + "description": "This protocol performs a custom nucleic acid purification using the Zymobiomics Magbead kit. This protocol was updated from this to APIv2.\n\n\n\nNEST Deep Well Plate or similar\nOpentrons P300 Single-channel electronic pipette\nOpentrons P300 Multi-channel electronic pipette\nOpentrons 300ul tipracks\n\n\n\nSTARTING SETUP for 4x6 2ml screwcap tube aluminum block (slot 2):\n* tubes A1-D6: original samples (up to 24 samples aligned down columns and then across rows)\nMID-PROTOCOL SETUP for 4x6 2ml screwcap tube aluminum block (slot 2):\n tubes A1-C1: molecular grade water tubes (1 tube for each 8 samples); note-- the user is prompted to replace these tubes midway through the protocol*\n12-channel reagent reservoir (slot 4):\n channel 1: mag binding buffer\n channel 2: magnetic beads\n channel 3: magwash 1\n channels 4-5: magwash 2 (1 channel each for 2x washes)\nwaste reservoir (slot 11):\n Note-- the reservoir is programmed as an Agilent 290ml single-channel reservoir, but the user can replace this with any reservoir of choice for containing the liquid waste throughout the protocol by calibrating to the top of the reservoir before the run.*", "internal": "7a1ae8", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7aa3fd-library-quantification/README.json b/protoBuilds/7aa3fd-library-quantification/README.json index 8700e386e..46e41fb9a 100644 --- a/protoBuilds/7aa3fd-library-quantification/README.json +++ b/protoBuilds/7aa3fd-library-quantification/README.json @@ -5,7 +5,7 @@ "Custom" ] }, - "description": "This protocol performs the QPCR plate set-up protocol for library quantification step of NGS library prep.\n\n\n\nEppendorf twin.tec 96-well PCR plate 150ul #0030128605\nOpentrons temperature module with 96-well aluminum block insert\nOpentrons 4-in-1 tuberack with 4x6 insert for 2ml Eppendorf snapcap tubes or equivalent.\nOpentrons 10ul and 200ul filter tipracks\nOpentrons GEN1 P10 and P300 single-channel electronic pipettes\n\n\n\n4x6 tuberack with 2ml Eppendorf snapcap tubes (slot 2)\n* tubes A1-A5: water\n* tube B1: QPCR mastermix", + "description": "This protocol performs the QPCR plate set-up protocol for library quantification step of NGS library prep.\n\n\n\nEppendorf twin.tec 96-well PCR plate 150ul #0030128605\nOpentrons temperature module with 96-well aluminum block insert\nOpentrons 4-in-1 tuberack with 4x6 insert for 2ml Eppendorf snapcap tubes or equivalent.\nOpentrons 10ul and 200ul filter tipracks\nOpentrons GEN1 P10 and P300 single-channel electronic pipettes\n\n\n\n4x6 tuberack with 2ml Eppendorf snapcap tubes (slot 2)\n tubes A1-A5: water\n tube B1: QPCR mastermix", "internal": "7aa3fd", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7aa3fd-size-selection/README.json b/protoBuilds/7aa3fd-size-selection/README.json index 76e1e642f..fbf78b1b8 100644 --- a/protoBuilds/7aa3fd-size-selection/README.json +++ b/protoBuilds/7aa3fd-size-selection/README.json @@ -5,7 +5,7 @@ "Custom" ] }, - "description": "This protocol performs the final size selection step of NGS library prep.\n\n\n\nEppendorf twin.tec 96-well PCR plate 150ul #0030128605\nOpentrons magnetic module\nOpentrons 4-in-1 tuberack with 4x6 insert for 2ml Eppendorf snapcap tubes or equivalent.\nOpentrons 10ul and 200ul filter tipracks\nOpentrons GEN1 P10 and P300 single-channel electronic pipettes\n\n\n\n4x6 tuberack with 2ml Eppendorf snapcap tubes (slot 2)\n* tube A1: SPRI beads\n* tube B1-B3: 80% ethanol\n* tube C1: Low EDTA TE", + "description": "This protocol performs the final size selection step of NGS library prep.\n\n\n\nEppendorf twin.tec 96-well PCR plate 150ul #0030128605\nOpentrons magnetic module\nOpentrons 4-in-1 tuberack with 4x6 insert for 2ml Eppendorf snapcap tubes or equivalent.\nOpentrons 10ul and 200ul filter tipracks\nOpentrons GEN1 P10 and P300 single-channel electronic pipettes\n\n\n\n4x6 tuberack with 2ml Eppendorf snapcap tubes (slot 2)\n tube A1: SPRI beads\n tube B1-B3: 80% ethanol\n* tube C1: Low EDTA TE", "internal": "7aa3fd", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7aad4e/README.json b/protoBuilds/7aad4e/README.json index 1adc25644..3dae3c180 100644 --- a/protoBuilds/7aad4e/README.json +++ b/protoBuilds/7aad4e/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Note: the protocol will read the csv source and destination slots to load labware onto the deck. Plates should always be placed in order of smaller deck number to large (i.e. place 384 plates in slots 1, 2, 3, and 4 if running 4 plates. If running one 96 plate, place it in slot 7 as opposed to 8).\n\n", - "description": "This protocol preps up to two 96 well plates with cell culture media from up to 6 source 384 well plates. The protocol will automatically parse through the csv to determine how many plates are on the deck, giving the user the ability to have flexibility in run size, however plates should still be placed in order of the deck slot numbers. Culture is pre-mixed with an airgap before transfer.\nExplanation of complex parameters below:\n* .CSV File: Here, you should upload a .csv file formatted in the following way, being sure to include the header line (do NOT have \"0\" in between well names i.e. \"A01\", it should be \"A1\")\n\n* P300 Mount: Specify which mount (left or right) to host the P300 pipette.\n", + "description": "This protocol preps up to two 96 well plates with cell culture media from up to 6 source 384 well plates. The protocol will automatically parse through the csv to determine how many plates are on the deck, giving the user the ability to have flexibility in run size, however plates should still be placed in order of the deck slot numbers. Culture is pre-mixed with an airgap before transfer.\nExplanation of complex parameters below:\n .CSV File: Here, you should upload a .csv file formatted in the following way, being sure to include the header line (do NOT have \"0\" in between well names i.e. \"A01\", it should be \"A1\")\n\n P300 Mount: Specify which mount (left or right) to host the P300 pipette.\n", "internal": "7aad4e", "labware": "\nCorning 96 well plate, flat\nPerkin Elmer 110ul 384 well plate, flat\nOpentrons 200ul Filter tips\n", "markdown": { diff --git a/protoBuilds/7ada78-pt2/README.json b/protoBuilds/7ada78-pt2/README.json index 21d1a5e8e..1d893cae4 100644 --- a/protoBuilds/7ada78-pt2/README.json +++ b/protoBuilds/7ada78-pt2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol preps and runs a PCR on the Opentrons thermocycler using a .csv input. RNA and NF water are added to the PCR plate, and mastermix is then added to the resulting solution and mixed. A pause is included after the RNA is added to the water in the thermocycler plate, and the user is prompted to replace the water plate with the same 96 well plate, but with mastermix in column 1. If the protocol runs out of tips, it will automatically stop and the user is prompted to replace tips. For csv information and formatting notes, see below.\nExplanation of complex parameters below:\n* Number of columns: Specify the number of columns in the thermocycler plate to dispense mastermix into. Mastermix will always come from column 1 of the 96 well plate on slot 3. The mastermix plate will replace with water plate on slot 3 after an automatic pause in the protocol.\n* .CSV File: Here, you should upload a .csv file formatted in the following way, being sure to include the header line\n(use slot 7 for the thermocycler slot, and input an \"x\" for values that are not needed in that row):\n\n* Pipette Mount: Specify which mount (left or right) to host the P20 Single, and Multi-channel pipettes, respectively.\n", + "description": "This protocol preps and runs a PCR on the Opentrons thermocycler using a .csv input. RNA and NF water are added to the PCR plate, and mastermix is then added to the resulting solution and mixed. A pause is included after the RNA is added to the water in the thermocycler plate, and the user is prompted to replace the water plate with the same 96 well plate, but with mastermix in column 1. If the protocol runs out of tips, it will automatically stop and the user is prompted to replace tips. For csv information and formatting notes, see below.\nExplanation of complex parameters below:\n Number of columns: Specify the number of columns in the thermocycler plate to dispense mastermix into. Mastermix will always come from column 1 of the 96 well plate on slot 3. The mastermix plate will replace with water plate on slot 3 after an automatic pause in the protocol.\n .CSV File: Here, you should upload a .csv file formatted in the following way, being sure to include the header line\n(use slot 7 for the thermocycler slot, and input an \"x\" for values that are not needed in that row):\n\n* Pipette Mount: Specify which mount (left or right) to host the P20 Single, and Multi-channel pipettes, respectively.\n", "internal": "7ada78-pt2", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 4-in-1 tube rack with 1.5mL Eppendoft snap cap tubes\nOpentrons 20ul Filter tips\n96-W Abgene Plate\n", "markdown": { diff --git a/protoBuilds/7cfbde/README.json b/protoBuilds/7cfbde/README.json index d64bad23d..402c4af8f 100644 --- a/protoBuilds/7cfbde/README.json +++ b/protoBuilds/7cfbde/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This protocol automates RNA extraction according to the 3D Black Bio RNA Extraction Kit.\n\nUsing the P300 Multi-Channel Pipette, this protocol can accommodate up to 96 samples per run and can be configured to run any multiple of 8 up to 96. Starting with at least 200\u00b5L of sample in a standard 96-well plate, the entire process is automated and ends with 60\u00b5L of elution containing RNA dispensed into a 96-well PCR plate. The elution is then ready for RT/qPCR, Next-Gen Sequencing, hybridization, etc.\n\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nOpentrons Magnetic Module, GEN2\nOpentrons P300 Multi-Channel Pipette\nOpentrons 200\u00b5L Filter Tips (recommended) or Opentrons 300\u00b5L Tips\nNEST 96-Deep Well Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir\nNEST 1-Well Reservoir\nOpentrons 96-Well Aluminum Block\nPCR Tubes\n3D Black Bio Extraction Kit\nSamples\n\n\n\nReagent Preparation\nPrepare all reagents according to manual.\n\nProteinase K: At least 10\u00b5L (12\u00b5L is recommended) per column of samples should fill a PCR Strip.\nThe PCR strip should be placed in column 1 of the Opentrons 96-Well Aluminum Block\n\nMagBeads: At least 20\u00b5L (22\u00b5L is recommended) per column of samples should fill 1 (or 2, if processing more than 48 samples) PCR strip(s).\nThe PCR strip(s) should be placed in column(s) 3 (and 4, if processing more than 48 samples) of the Opentrons 96-Well Aluminum Block\n\nLysis-Binding Mix: In slots 1-6 of the NEST 12-Well Reservoir.\nFor every column (8 samples), 7mL of Lysis-Binding Mix should be added to the reservoir. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 1 would get 14mL lysis-binding mix, slot 2 would get 7mL lysis-binding mix, slot 3 would be empty, etc).\n\nWash 1: In slots 7-12 of the NEST 12-Well Reservoir.\nFor every column (8 samples), 6.5mL of wash 1 should be added to the reservoir. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 7 would get 13mL wash 1, slot 8 would get 6.5mL wash 1, slot 9 would be empty, etc).\n\nWash 2: In NEST 1-Well Reservoir.\nFor every column (8 samples), 14mL of wash 2 should be added to the reservoir.\n\nElution Buffer: At least 60\u00b5L (65\u00b5L is recommended) per column of samples should fill a PCR Strip. Each PCR strip can accommodate up to two columns worth (16) samples.\nThe PCR strips should be loaded in columns 7-12 of the Opentrons 96-Well Aluminum Block\n\n\nDeck Layout\n\nSlot 1: NEST 96-Well PCR Plate, containing samples\nSlot 2: NEST 1-Well Reservoir containing Wash 2\nSlot 3: Opentrons 200\u00b5L Filter Tips\nSlot 4: Opentrons 96-Well Aluminum Block containing Proteinase K, Magnetic Beads, and Elution Buffer\nSlot 5: NEST 12-Well Reservoir containing Lysis-Binding Mix and Wash 1\nSlot 6: Opentrons 200\u00b5L Filter Tips\nSlot 7: Opentrons Magnetic Module, GEN2 with NEST 96-Deep Well Plate, 2mL\nSlot 8: Opentrons 200\u00b5L Filter Tips\nSlot 9: Opentrons 200\u00b5L Filter Tips\nSlot 10: NEST 1-Well Reservoir, empty for liquid waste\nSlot 11: NEST 1-Well Reservoir, empty for liquid waste\n\nNote about tips: The tips in slot 8 will be used for removing supernatant and used tips will be returned to empty tip racks to prevent overflow of the waste bin.\n\nUsing the customizations field (below), set up your protocol.\n* P300-Multi Mount: Select which mount the P300-Multi is attached to\n* Number of Samples: Specify the number of samples to run", + "description": "This protocol automates RNA extraction according to the 3D Black Bio RNA Extraction Kit.\n\nUsing the P300 Multi-Channel Pipette, this protocol can accommodate up to 96 samples per run and can be configured to run any multiple of 8 up to 96. Starting with at least 200\u00b5L of sample in a standard 96-well plate, the entire process is automated and ends with 60\u00b5L of elution containing RNA dispensed into a 96-well PCR plate. The elution is then ready for RT/qPCR, Next-Gen Sequencing, hybridization, etc.\n\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 4.0.0 or later)\nOpentrons Magnetic Module, GEN2\nOpentrons P300 Multi-Channel Pipette\nOpentrons 200\u00b5L Filter Tips (recommended) or Opentrons 300\u00b5L Tips\nNEST 96-Deep Well Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir\nNEST 1-Well Reservoir\nOpentrons 96-Well Aluminum Block\nPCR Tubes\n3D Black Bio Extraction Kit\nSamples\n\n\n\nReagent Preparation\nPrepare all reagents according to manual.\n\nProteinase K: At least 10\u00b5L (12\u00b5L is recommended) per column of samples should fill a PCR Strip.\nThe PCR strip should be placed in column 1 of the Opentrons 96-Well Aluminum Block\n\nMagBeads: At least 20\u00b5L (22\u00b5L is recommended) per column of samples should fill 1 (or 2, if processing more than 48 samples) PCR strip(s).\nThe PCR strip(s) should be placed in column(s) 3 (and 4, if processing more than 48 samples) of the Opentrons 96-Well Aluminum Block\n\nLysis-Binding Mix: In slots 1-6 of the NEST 12-Well Reservoir.\nFor every column (8 samples), 7mL of Lysis-Binding Mix should be added to the reservoir. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 1 would get 14mL lysis-binding mix, slot 2 would get 7mL lysis-binding mix, slot 3 would be empty, etc).\n\nWash 1: In slots 7-12 of the NEST 12-Well Reservoir.\nFor every column (8 samples), 6.5mL of wash 1 should be added to the reservoir. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 7 would get 13mL wash 1, slot 8 would get 6.5mL wash 1, slot 9 would be empty, etc).\n\nWash 2: In NEST 1-Well Reservoir.\nFor every column (8 samples), 14mL of wash 2 should be added to the reservoir.\n\nElution Buffer: At least 60\u00b5L (65\u00b5L is recommended) per column of samples should fill a PCR Strip. Each PCR strip can accommodate up to two columns worth (16) samples.\nThe PCR strips should be loaded in columns 7-12 of the Opentrons 96-Well Aluminum Block\n\n\nDeck Layout\n\nSlot 1: NEST 96-Well PCR Plate, containing samples\nSlot 2: NEST 1-Well Reservoir containing Wash 2\nSlot 3: Opentrons 200\u00b5L Filter Tips\nSlot 4: Opentrons 96-Well Aluminum Block containing Proteinase K, Magnetic Beads, and Elution Buffer\nSlot 5: NEST 12-Well Reservoir containing Lysis-Binding Mix and Wash 1\nSlot 6: Opentrons 200\u00b5L Filter Tips\nSlot 7: Opentrons Magnetic Module, GEN2 with NEST 96-Deep Well Plate, 2mL\nSlot 8: Opentrons 200\u00b5L Filter Tips\nSlot 9: Opentrons 200\u00b5L Filter Tips\nSlot 10: NEST 1-Well Reservoir, empty for liquid waste\nSlot 11: NEST 1-Well Reservoir, empty for liquid waste\n\nNote about tips: The tips in slot 8 will be used for removing supernatant and used tips will be returned to empty tip racks to prevent overflow of the waste bin.\n\nUsing the customizations field (below), set up your protocol.\n P300-Multi Mount: Select which mount the P300-Multi is attached to\n Number of Samples: Specify the number of samples to run", "internal": "7cfbde", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7f0f89/README.json b/protoBuilds/7f0f89/README.json index 965c0856c..333762a8c 100644 --- a/protoBuilds/7f0f89/README.json +++ b/protoBuilds/7f0f89/README.json @@ -5,7 +5,7 @@ "Plate Filling" ] }, - "description": "This protocol transfers a specified volume of developer solution into reservoir cartridges within a custom 216-well plate. The developer solution is aspirated from a Nest 195mL reservoir, then distributed to the 216-well plate down by column. Transfers are distributed in chunks of 3 between the reservoir and plate, with a delay and blow out step for viscous liquid considerations. Extra developer solution is aspirated to ensure that each cartridge receives adequate distribution.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Single-Channel Pipette\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nNest 1-Well Reservoir 195 mL\nInvoy 216-Well Cartridge Plate\nInvoy Canisters with Fibrous Reservoir\n\n\n\nSlots 1, 2, 4, 5, 7, 8, 10, 11: Invoy 216-Well Cartridge Plate\nSlot 6: Opentrons 96 Tip Rack 300 \u00b5L\nSlot 9: Nest 1-Well Reservoir 195 mL\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify the number of samples in your protocol run.\n* Dispense Height Above Cartridge: Specify the height (mm) above the cartridge the pipette will dispense liquid\n* Dispense Volume: Specify the volume (\u00b5L) of developer solution dispensed into each cartridge\n* Dispense Flow Rate: Specify the rate (\u00b5L/sec) at which the pipette will aspirate solution into each cartridge\n* Dispense Flow Rate: Specify the rate (\u00b5L/sec) at which the pipette will dispense solution into each cartridge\n* Aspirate Delay Time: Specify the time to delay after each aspiration (in seconds)\n* Dispense Delay Time: Specify the time to delay after each dispense (in seconds)\n* P300 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette", + "description": "This protocol transfers a specified volume of developer solution into reservoir cartridges within a custom 216-well plate. The developer solution is aspirated from a Nest 195mL reservoir, then distributed to the 216-well plate down by column. Transfers are distributed in chunks of 3 between the reservoir and plate, with a delay and blow out step for viscous liquid considerations. Extra developer solution is aspirated to ensure that each cartridge receives adequate distribution.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons P300 Single-Channel Pipette\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 300\u00b5L Tips\nNest 1-Well Reservoir 195 mL\nInvoy 216-Well Cartridge Plate\nInvoy Canisters with Fibrous Reservoir\n\n\n\nSlots 1, 2, 4, 5, 7, 8, 10, 11: Invoy 216-Well Cartridge Plate\nSlot 6: Opentrons 96 Tip Rack 300 \u00b5L\nSlot 9: Nest 1-Well Reservoir 195 mL\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify the number of samples in your protocol run.\n Dispense Height Above Cartridge: Specify the height (mm) above the cartridge the pipette will dispense liquid\n Dispense Volume: Specify the volume (\u00b5L) of developer solution dispensed into each cartridge\n Dispense Flow Rate: Specify the rate (\u00b5L/sec) at which the pipette will aspirate solution into each cartridge\n Dispense Flow Rate: Specify the rate (\u00b5L/sec) at which the pipette will dispense solution into each cartridge\n Aspirate Delay Time: Specify the time to delay after each aspiration (in seconds)\n Dispense Delay Time: Specify the time to delay after each dispense (in seconds)\n P300 Single GEN2 Mount: Specify the mount side for the P300 Single GEN2 pipette", "internal": "7f0f89", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/7f9595/README.json b/protoBuilds/7f9595/README.json index 7dffe9796..a8e760380 100644 --- a/protoBuilds/7f9595/README.json +++ b/protoBuilds/7f9595/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol automates the serial dilution of two separate sample columns and also adds PBS buffer to the necessary wells. It will perform additional mixing steps before and after the addition of reagents. Each transfer performs a blow out in the destination well.\nSerial Dilution Plate Map:\n\nExplanation of parameters below:\n* P300 Multichannel GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n* Reservoir Type: Specify the type of reservoir being used in Slot 1.\n* Blowout Height from Well Bottom (mm): The height the blowout should occur from the bottom of the well. For example, a volume of 200 uL in this plate will have a height of approximately 5.4 mm from the bottom of the well.\n* Mix Aspiration Flow Rate (uL/s): Flow rate when aspiration occurs in a mixing step.\n* Mix Dispensing Flow Rate (uL/s): Flow rate when dispensing occurs in a mixing step.\n", + "description": "This protocol automates the serial dilution of two separate sample columns and also adds PBS buffer to the necessary wells. It will perform additional mixing steps before and after the addition of reagents. Each transfer performs a blow out in the destination well.\nSerial Dilution Plate Map:\n\nExplanation of parameters below:\n P300 Multichannel GEN2 Mount: Specify which mount (left or right) to load the P300 multi channel pipette.\n Reservoir Type: Specify the type of reservoir being used in Slot 1.\n Blowout Height from Well Bottom (mm): The height the blowout should occur from the bottom of the well. For example, a volume of 200 uL in this plate will have a height of approximately 5.4 mm from the bottom of the well.\n Mix Aspiration Flow Rate (uL/s): Flow rate when aspiration occurs in a mixing step.\n* Mix Dispensing Flow Rate (uL/s): Flow rate when dispensing occurs in a mixing step.\n", "internal": "7f9595", "labware": "\nCorning 96 Well Plate 360 \u00b5L Flat\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 300uL Tips\n", "markdown": { diff --git a/protoBuilds/7fc7b1/README.json b/protoBuilds/7fc7b1/README.json index a14600ea4..2c5ae47e2 100644 --- a/protoBuilds/7fc7b1/README.json +++ b/protoBuilds/7fc7b1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Example Deck Layout:\n\n", - "description": "With this protocol, your robot can perform a custom PCR preparation using a P20-multi pipette.\nThis protocol allows you to choose which slots and plate (96 or 384 well) will be destination plates, and also gives the option to choose between a reservoir and 96 well plate as source plates for mastermix.\nAll available empty slots will be filled with tipracks, and the user will be prompted to refill the tipracks if all are emptied in the middle of the protocol.\nExplanation of complex parameters below:\n* .csv file: Upload a .csv file formatted in the following way, being sure to include the header line.\n* Mastermix Labware: Specify whether you are using a 12-channel NEST 15mL reservoir or Greiner Bio-One 96-Well Plates 200\u00b5l well plate as the mastermix source. If you choose a 12-channel reservoir for mastermix, the mastermix should be filled in the first channel of the reservoir alone. If you choose a 96-well plate for mastermix, the mastermix should be filled in the first columns in as many columns as necessary. The protocol will automatically calculate when the second column should be acccessed for mastermix once the first column has run out of volume, then the third column, etc.\n* Mastermix Plate Slot: Specify which slot the mastermix will be on the deck.\n* Mastermix Volume Loaded in Source: Specify the volume of mastermix per column in ul.\n* Mastermix Starting Column: Specify the column in which populated mastermix columns start.\n* DNA Volume: Specify the DNA volume (in ul) to which mastermix will be added.\n* Transfer Scheme: Specify whether the transfer scheme will be multi-dispense or single dispense (distribution vs 1-1 transfer).\n* P20-multi GEN2 mount: Specify which mount (left or right) the P20 Multi-GEN2 mount will be.\n", + "description": "With this protocol, your robot can perform a custom PCR preparation using a P20-multi pipette.\nThis protocol allows you to choose which slots and plate (96 or 384 well) will be destination plates, and also gives the option to choose between a reservoir and 96 well plate as source plates for mastermix.\nAll available empty slots will be filled with tipracks, and the user will be prompted to refill the tipracks if all are emptied in the middle of the protocol.\nExplanation of complex parameters below:\n .csv file: Upload a .csv file formatted in the following way, being sure to include the header line.\n Mastermix Labware: Specify whether you are using a 12-channel NEST 15mL reservoir or Greiner Bio-One 96-Well Plates 200\u00b5l well plate as the mastermix source. If you choose a 12-channel reservoir for mastermix, the mastermix should be filled in the first channel of the reservoir alone. If you choose a 96-well plate for mastermix, the mastermix should be filled in the first columns in as many columns as necessary. The protocol will automatically calculate when the second column should be acccessed for mastermix once the first column has run out of volume, then the third column, etc.\n Mastermix Plate Slot: Specify which slot the mastermix will be on the deck.\n Mastermix Volume Loaded in Source: Specify the volume of mastermix per column in ul.\n Mastermix Starting Column: Specify the column in which populated mastermix columns start.\n DNA Volume: Specify the DNA volume (in ul) to which mastermix will be added.\n Transfer Scheme: Specify whether the transfer scheme will be multi-dispense or single dispense (distribution vs 1-1 transfer).\n P20-multi GEN2 mount: Specify which mount (left or right) the P20 Multi-GEN2 mount will be.\n", "internal": "7fc7b1", "labware": "\nGreiner Bio-One 96-Well Plates 200\u00b5l #652290\nSarstedt 384-Well Plates 40\u00b5l #72.1984.202\nNest 12-Well Reservoir 15mL\nOpentrons 20\u00b5l tipracks\n", "markdown": { diff --git a/protoBuilds/925d07-cp/README.json b/protoBuilds/925d07-cp/README.json index c81a5aef2..4793c3843 100644 --- a/protoBuilds/925d07-cp/README.json +++ b/protoBuilds/925d07-cp/README.json @@ -5,7 +5,7 @@ "Aliquoting" ] }, - "description": "Links:\n* Random Aliquoting\n\n\n* Plasmind Luciferase Assay\n\n\n* QIAcuity Plate Transfer\n\n\n* PCR Prep\n\n\nThis protocol performs a custom aliquoting procedure based on a randomly-generated 1-4 plate map. Enough volume to accommodate all 4 destination wells, including overage volume, is aspirated from the source well and distributed to all 4 destination wells. A new tip is obtained for each source-destination set. The layout is shown below: \n\nThe proper pipette (P20 or P300) is selected automatically based on the input siRNA volume.\n", + "description": "Links:\n Random Aliquoting\n\n\n Plasmind Luciferase Assay\n\n\n QIAcuity Plate Transfer\n\n\n PCR Prep\n\n\nThis protocol performs a custom aliquoting procedure based on a randomly-generated 1-4 plate map. Enough volume to accommodate all 4 destination wells, including overage volume, is aspirated from the source well and distributed to all 4 destination wells. A new tip is obtained for each source-destination set. The layout is shown below: \n\nThe proper pipette (P20 or P300) is selected automatically based on the input siRNA volume.\n", "internal": "925d07", "labware": "\nEppendorf V-bottom, Lo-Bind 96-well plates #0030603303\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/925d07-pla/README.json b/protoBuilds/925d07-pla/README.json index 914b6f0a9..568a71b97 100644 --- a/protoBuilds/925d07-pla/README.json +++ b/protoBuilds/925d07-pla/README.json @@ -5,8 +5,8 @@ "PCR Prep" ] }, - "deck-setup": "\n* reservoir channel 1: lipofectamine 2000\n* reservoir channel 2: V141 plasmid\n* 96-wellplate: siRNA\n", - "description": "Links:\n* Random Aliquoting\n\n\n* Plasmind Luciferase Assay\n\n\n* QIAcuity Plate Transfer\n\n\n* PCR Prep\n\n\nThis protocol performs a custom Plasmid Luciferase Assay to a 384-wellplate.\n", + "deck-setup": "\n reservoir channel 1: lipofectamine 2000\n reservoir channel 2: V141 plasmid\n* 96-wellplate: siRNA\n", + "description": "Links:\n Random Aliquoting\n\n\n Plasmind Luciferase Assay\n\n\n QIAcuity Plate Transfer\n\n\n PCR Prep\n\n\nThis protocol performs a custom Plasmid Luciferase Assay to a 384-wellplate.\n", "internal": "9250d7", "labware": "\nCorning 96 Well Plate 360 ul Flat\nCustom 384 Well Plate 100 ul\nNEST 12-Well Reservoirs, 15 mL #999-00076\nOpentrons 20ul tips\n", "markdown": { diff --git a/protoBuilds/925d07-q/README.json b/protoBuilds/925d07-q/README.json index 22a8b0466..d8aaab814 100644 --- a/protoBuilds/925d07-q/README.json +++ b/protoBuilds/925d07-q/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Random Aliquoting\n\n\n* Plasmind Luciferase Assay\n\n\n* QIAcuity Plate Transfer\n\n\n* PCR Prep\n\n\nThis protocol performs a custom QIAcuity PCR prep.\n", + "description": "Links:\n Random Aliquoting\n\n\n Plasmind Luciferase Assay\n\n\n QIAcuity Plate Transfer\n\n\n PCR Prep\n\n\nThis protocol performs a custom QIAcuity PCR prep.\n", "internal": "9250d7", "labware": "\nOpentrons 20ul tips\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nQIAcuity 96-well Nanoplate\n", "markdown": { diff --git a/protoBuilds/925d07-v3/README.json b/protoBuilds/925d07-v3/README.json index b21b62fc3..b80cdb262 100644 --- a/protoBuilds/925d07-v3/README.json +++ b/protoBuilds/925d07-v3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "Links:\n* Random Aliquoting\n\n\n* Plasmind Luciferase Assay\n\n\n* QIAcuity Plate Transfer\n\n\n* PCR Prep\n\n\nThis protocol performs a custom PCR prep from 4 source 96-well RNA plate to a single 384-well destination plate. The transfer scheme is shown below.\n", + "description": "Links:\n Random Aliquoting\n\n\n Plasmind Luciferase Assay\n\n\n QIAcuity Plate Transfer\n\n\n PCR Prep\n\n\nThis protocol performs a custom PCR prep from 4 source 96-well RNA plate to a single 384-well destination plate. The transfer scheme is shown below.\n", "internal": "9250d7", "labware": "\nOpentrons 20ul tips\nCorning 96 Well Plate 360 ul Flat\nCustom 384 Well Plate 100 ul\nGeneric PCR Strips in 96-well aluminum block\n", "markdown": { diff --git a/protoBuilds/9778eb/README.json b/protoBuilds/9778eb/README.json index 7c4bb8b9d..3dd7d71a9 100644 --- a/protoBuilds/9778eb/README.json +++ b/protoBuilds/9778eb/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This is a custom implementation of the Mag-Bind Blood and Tissue kit. Specify the starting sample volume, final elution volume, and number of samples, allowing the OT-2 to automate the procedure with minimal intervention to empty trash and/or refill tip racks as alerted.\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Initial Volume: Specify starting volume of sample (ul).\n* Elution Volume: Specify elution volume (ul) into final plate.\n* Flash on Robot Pause: Specify whether the robot will flash on pause. This includes trash or tip rack notifications\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "This is a custom implementation of the Mag-Bind Blood and Tissue kit. Specify the starting sample volume, final elution volume, and number of samples, allowing the OT-2 to automate the procedure with minimal intervention to empty trash and/or refill tip racks as alerted.\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Initial Volume: Specify starting volume of sample (ul).\n Elution Volume: Specify elution volume (ul) into final plate.\n Flash on Robot Pause: Specify whether the robot will flash on pause. This includes trash or tip rack notifications\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "9778eb", "labware": "\nNEST 96 Wellplate 2mL\nNEST 12 Reservoir 15mL\nOpentrons 200uL Filter Tips\nThermofisher 96 Well, semi-skirted, black lettering mounted to deck with Opentrons 96 Aluminum block\n", "markdown": { diff --git a/protoBuilds/9778eb_mass_norm/README.json b/protoBuilds/9778eb_mass_norm/README.json index d19170dba..c710860a3 100644 --- a/protoBuilds/9778eb_mass_norm/README.json +++ b/protoBuilds/9778eb_mass_norm/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nReagent Color Code\n\n\n\nStarting deck layout with reagents\n\n\n", - "description": "This protocol uses values in a CSV to normalize samples in a 96 well plate. The CSV requires starting and finishing concentrations broken up into mass/moles and volumes. This allows for minimal user calculations before loading samples. Additionally, units can be different from run to run and even sample to sample provided the starting and finishing units are the same. E.g. sample A1 is nanograms/uL and will be diluted to a set concentration in well A1 in the normalized plate while sample B1 is moles/uL and will be diluted to a set molarity in well B1.\nThis protocol also checks if normalization is possible with the given concentrations and will list the failed wells at the end of the protocol run. E.g. C1 starting concentration is 15 ng/uL and the stated final concentration target is 20 ng/uL so C1 will be added to the 'failed well' list at the protocol end.\nExplanation of complex parameters below:\n* Volume of Water in Falcon Tube: Starting volume of nuclease free water in the on-deck tube rack. This is in mL and will be used to track liquid height\n* Source Plate Type: 96 well plate samples will start the protocol in\n* Destination Plate Type: 96 well plate samples will end the protocol in\n* P20 Single GEN2 Mount: Defines which side the P20 single pipette will be mounted on. The P300 single pipette will be mounted on the opposite side\n* Transfer .csv File: Here, you should upload a .csv file formatted like the example CSV located here\n", + "description": "This protocol uses values in a CSV to normalize samples in a 96 well plate. The CSV requires starting and finishing concentrations broken up into mass/moles and volumes. This allows for minimal user calculations before loading samples. Additionally, units can be different from run to run and even sample to sample provided the starting and finishing units are the same. E.g. sample A1 is nanograms/uL and will be diluted to a set concentration in well A1 in the normalized plate while sample B1 is moles/uL and will be diluted to a set molarity in well B1.\nThis protocol also checks if normalization is possible with the given concentrations and will list the failed wells at the end of the protocol run. E.g. C1 starting concentration is 15 ng/uL and the stated final concentration target is 20 ng/uL so C1 will be added to the 'failed well' list at the protocol end.\nExplanation of complex parameters below:\n Volume of Water in Falcon Tube: Starting volume of nuclease free water in the on-deck tube rack. This is in mL and will be used to track liquid height\n Source Plate Type: 96 well plate samples will start the protocol in\n Destination Plate Type: 96 well plate samples will end the protocol in\n P20 Single GEN2 Mount: Defines which side the P20 single pipette will be mounted on. The P300 single pipette will be mounted on the opposite side\n* Transfer .csv File: Here, you should upload a .csv file formatted like the example CSV located here\n", "internal": "9778eb_mass_norm", "labware": "\nOpentrons 6 Tube Rack with Falcon 50 mL Conical\nNEST 96 Deepwell Plate 2mL\nNEST 100uL 96 Well Plate\nThermofisher Semi-Skirted on Adapter 96 Well Plate\n", "markdown": { diff --git a/protoBuilds/9778eb_spri/README.json b/protoBuilds/9778eb_spri/README.json index ea5080f7d..f625766e9 100644 --- a/protoBuilds/9778eb_spri/README.json +++ b/protoBuilds/9778eb_spri/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nReagent Color Code\n\n\n\nStarting deck layout with reagents for single bead purification\n\n\n\nSlot 1: 96 Filter Tip Rack 20 uL\n\nSlot 2: 96 Filter Tip Rack 200 uL\nSlot 3: Custom 3D printed custom adapter for half-skirted plates with Thermofisher half-skirted plate\nSlot 4: NEST 1 Well Reservoir 195 mL\nSlot 5: NEST 12 Well Reservoir 15 mL\nSlot 6: Empty\nSlot 7: Magnetic module with custom 3D printed custom adapter for half-skirted plates with Thermofisher half-skirted plate\nSlot 8: 96 Filter Tip Rack 20 uL\nSlot 9: 96 Filter Tip Rack 200 uL\nSlot 10: 96 Filter Tip Rack 20 uL\n\nSlot 11: 96 Filter Tip Rack 200 uL\n\n\nStarting deck layout with reagents for size selection\n\n\n\nSlot 1: 96 Filter Tip Rack 20 uL\n\nSlot 2: 96 Filter Tip Rack 200 uL\nSlot 3: Custom 3D printed custom adapter for half-skirted plates with Thermofisher half-skirted plate\nSlot 4: NEST 1 Well Reservoir 195 mL\nSlot 5: NEST 12 Well Reservoir 15 mL\nSlot 6: Magnetic module with custom 3D printed custom adapter for half-skirted plates with Thermofisher half-skirted plate\nSlot 7: Magnetic module with custom 3D printed custom adapter for half-skirted plates with Thermofisher half-skirted plate\nSlot 8: 96 Filter Tip Rack 20 uL\nSlot 9: 96 Filter Tip Rack 200 uL\nSlot 10: 96 Filter Tip Rack 20 uL\nSlot 11: 96 Filter Tip Rack 200 uL\n\n", - "description": "This protocol purifies samples using SPRI beads with an option to perform a size selection with two separate bead ratios. Size selection requires two magnetic modules.\nBeads are added at a specified ratio to the samples, mixed, and left to incubate. If size selection is to be performed, the supernatant is then removed to the second magnetic module for a second bead purification where the resulting supernatant is removed to the liquid waste.\nAfter bead purification(s), two 200uL ethanol washes are performed. The beads are left to air dry for a set amount of time before a set volume of elution liquid is added, mixed with the beads, left to incubate for a set time, and separated from the beads. This supernatant is removed to an awaiting plate in slot 3.\nExplanation of complex parameters below:\n* Number of Samples: How many samples are in the starting 96 well plate, 1-96 allowed. Multiples of 8 for full columns will have the most efficient reagent use\n* Initial Sample Volume: Volume in uL for starting samples. This is used to help calculate bead volume addition\n* Bead Ratio 1: Bead to sample ratio used to calculate bead volume addition. First addition for size selection and only addition for non-size selection\n* Bead Ratio 2: Bead to sample ratio used to calculate bead volume addition for second bead addition during size selection. This is not used during non-size selection protocols with a single bead addition\n* Transfer Volume: During size selection, how much volume to transfer from first magnetic module plate to second. This is needed to properly calculate second bead addition volume for proper size selection\n* Bead Air Dry Time: How many minutes beads will be left to air dry after ethanol wash steps. Default is 10 minutes\n* Bead Incubation Time: How many minutes beads will be left to incubate with samples during first and second addition. Default is 5 minutes\n* Bead Separation Time: How many minutes beads will be left to separate on the magnetic module. Default is 5 minutes\n* Elution Solution Volume: How much liquid will be added to washed and dried beads for elution. Default volume is 50 uL\n* Elution Time: How many minutes the elution solution will incubate with the beads. Default is 10 minutes\n* Final Plate Volume: How much liquid will be transferred from the beads mixed with elution liquid to final elution plate in slot 3. Default is 50 uL\n* Flash Robot on Pause: Set whether the OT-2 will flash when trash is full, tips need refilling, or general user intervention is needed. Default is flashing.\n* P300 Multi Channel Pipette Mount: Select which mount side the p300 multichannel pipette is connected to. Default is left. The p20 multichannel will be set to the opposite side.\n* Size Selection or Single Purification: Select whether the OT-2 will perform a single bead purification with one magnetic module or a dual bead ratio-based size selection with two magnetic modules. Default is size selection.\n", + "description": "This protocol purifies samples using SPRI beads with an option to perform a size selection with two separate bead ratios. Size selection requires two magnetic modules.\nBeads are added at a specified ratio to the samples, mixed, and left to incubate. If size selection is to be performed, the supernatant is then removed to the second magnetic module for a second bead purification where the resulting supernatant is removed to the liquid waste.\nAfter bead purification(s), two 200uL ethanol washes are performed. The beads are left to air dry for a set amount of time before a set volume of elution liquid is added, mixed with the beads, left to incubate for a set time, and separated from the beads. This supernatant is removed to an awaiting plate in slot 3.\nExplanation of complex parameters below:\n Number of Samples: How many samples are in the starting 96 well plate, 1-96 allowed. Multiples of 8 for full columns will have the most efficient reagent use\n Initial Sample Volume: Volume in uL for starting samples. This is used to help calculate bead volume addition\n Bead Ratio 1: Bead to sample ratio used to calculate bead volume addition. First addition for size selection and only addition for non-size selection\n Bead Ratio 2: Bead to sample ratio used to calculate bead volume addition for second bead addition during size selection. This is not used during non-size selection protocols with a single bead addition\n Transfer Volume: During size selection, how much volume to transfer from first magnetic module plate to second. This is needed to properly calculate second bead addition volume for proper size selection\n Bead Air Dry Time: How many minutes beads will be left to air dry after ethanol wash steps. Default is 10 minutes\n Bead Incubation Time: How many minutes beads will be left to incubate with samples during first and second addition. Default is 5 minutes\n Bead Separation Time: How many minutes beads will be left to separate on the magnetic module. Default is 5 minutes\n Elution Solution Volume: How much liquid will be added to washed and dried beads for elution. Default volume is 50 uL\n Elution Time: How many minutes the elution solution will incubate with the beads. Default is 10 minutes\n Final Plate Volume: How much liquid will be transferred from the beads mixed with elution liquid to final elution plate in slot 3. Default is 50 uL\n Flash Robot on Pause: Set whether the OT-2 will flash when trash is full, tips need refilling, or general user intervention is needed. Default is flashing.\n P300 Multi Channel Pipette Mount: Select which mount side the p300 multichannel pipette is connected to. Default is left. The p20 multichannel will be set to the opposite side.\n Size Selection or Single Purification: Select whether the OT-2 will perform a single bead purification with one magnetic module or a dual bead ratio-based size selection with two magnetic modules. Default is size selection.\n", "internal": "9778eb_spri", "labware": "\nNEST 12 Well Reservoir 15 mL\nNEST 1 Well Reservoir 195 mL\nCustom 3D printed custom adapter for half-skirted plates with below half-skirted plate\nThermofisher PCR Plate, 96-well, semi-skirted, flat deck, black lettering\n", "markdown": { diff --git a/protoBuilds/Opentrons_Logo/README.json b/protoBuilds/Opentrons_Logo/README.json index f5e84655c..f585083d2 100644 --- a/protoBuilds/Opentrons_Logo/README.json +++ b/protoBuilds/Opentrons_Logo/README.json @@ -5,7 +5,7 @@ "Opentrons Logo" ] }, - "description": "This is a demo protocol that will help you to get more familiar with your new OT-2! All you need is some food dye, a 96-well plate, and a 12-row trough or tube rack with 1.5mL or 2mL tubes. Your robot will pipette the Opentrons logo into your plate and you'll be ready to go!\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\n96-Well Microplate\n12-Row Trough or Tube Rack with 1.5mL/2mL Tubes\nWater and Food Dye (Two Colors)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nFor this demo protocol, you need a clean, empty 96-well plate (where the Opentrons logo will be created) and either a 12-row trough or 1.5mL/2mL tubes in a tube rack to store the water and food dye solution.\nIf using a 12-row trough, the two food dye solutions should be stored in column 1 and column 2. If using the tube rack, dye 1 should be stored in 'A1' & 'B1' and dye 2 should be stored in 'C1' & 'D1'.\nUsing the customization fields below, set up your protocol.\n* Pipette Model: Select which pipette you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n* Destination Plate Type: Select which (destination) plate you will use for this protocol.\n* Dye Labware Type: Select which (source) labware you will use for this protocol.", + "description": "This is a demo protocol that will help you to get more familiar with your new OT-2! All you need is some food dye, a 96-well plate, and a 12-row trough or tube rack with 1.5mL or 2mL tubes. Your robot will pipette the Opentrons logo into your plate and you'll be ready to go!\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\n96-Well Microplate\n12-Row Trough or Tube Rack with 1.5mL/2mL Tubes\nWater and Food Dye (Two Colors)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nFor this demo protocol, you need a clean, empty 96-well plate (where the Opentrons logo will be created) and either a 12-row trough or 1.5mL/2mL tubes in a tube rack to store the water and food dye solution.\nIf using a 12-row trough, the two food dye solutions should be stored in column 1 and column 2. If using the tube rack, dye 1 should be stored in 'A1' & 'B1' and dye 2 should be stored in 'C1' & 'D1'.\nUsing the customization fields below, set up your protocol.\n Pipette Model: Select which pipette you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n Destination Plate Type: Select which (destination) plate you will use for this protocol.\n Dye Labware Type: Select which (source) labware you will use for this protocol.", "internal": "Demo Protocol 1", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/arcis-multi-test/README.json b/protoBuilds/arcis-multi-test/README.json index ef420d319..12f3f3988 100644 --- a/protoBuilds/arcis-multi-test/README.json +++ b/protoBuilds/arcis-multi-test/README.json @@ -5,7 +5,7 @@ "Arcis Blood Kit" ] }, - "description": "Note: This is an updated version (apiV1 to apiV2) of this protocol\nThis protocol is designed for running tests with the Arcis Blood Kit with Opentrons Multi-Channel Pipettes and a 12-channel trough. (further instructions about the protocol can be found here). With the Arcis Blood Kit, nucleic acid investigations can be performed easily and efficiently with the two included reagents. This protocol calls for the use of a P50-Multi and P300-Multi pipettes, as well as a 12-channel reservoir (USA Scientific), Corning 96-well, 360\u03bcL flat plate, and two Bioplastics 100\u03bcL plates.\n\n\n\nArcis Blood Kit\nOpentrons P50 Multi-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50uL/300uL Tips\nUSA Scientific 12-Channel Reservoir\nCorning 96-Well Plate 360\u00b5L, Flat\nBioplastics 8-Tube Strip Mat, 100\u00b5L\nSamples\n\n\n\nSlot 1: Corning 360\u00b5L Plate, clean and empty\nSlot 2: Bioplastics Plate (in holder), clean and empty\nSlot 3: Bioplastics Plate (in holder), clean and empty\nSlot 4: 12-Channel Reservoir\n* Channel 1: Reagent 1 (150\u00b5L per sample, 15mL for full plate)\n* Channel 2: Reagent 2 (20\u00b5L per sample, 2mL for full plate)\n* Channel 3: MasterMix (20\u00b5L per sample, 2mL for full plate)\n* Channel 4: Sample (30\u00b5L per sample, 3mL for full plate)\nSlot 5: Opentrons Tips\nSlot 6: Opentrons Tips", + "description": "Note: This is an updated version (apiV1 to apiV2) of this protocol\nThis protocol is designed for running tests with the Arcis Blood Kit with Opentrons Multi-Channel Pipettes and a 12-channel trough. (further instructions about the protocol can be found here). With the Arcis Blood Kit, nucleic acid investigations can be performed easily and efficiently with the two included reagents. This protocol calls for the use of a P50-Multi and P300-Multi pipettes, as well as a 12-channel reservoir (USA Scientific), Corning 96-well, 360\u03bcL flat plate, and two Bioplastics 100\u03bcL plates.\n\n\n\nArcis Blood Kit\nOpentrons P50 Multi-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons 50uL/300uL Tips\nUSA Scientific 12-Channel Reservoir\nCorning 96-Well Plate 360\u00b5L, Flat\nBioplastics 8-Tube Strip Mat, 100\u00b5L\nSamples\n\n\n\nSlot 1: Corning 360\u00b5L Plate, clean and empty\nSlot 2: Bioplastics Plate (in holder), clean and empty\nSlot 3: Bioplastics Plate (in holder), clean and empty\nSlot 4: 12-Channel Reservoir\n Channel 1: Reagent 1 (150\u00b5L per sample, 15mL for full plate)\n Channel 2: Reagent 2 (20\u00b5L per sample, 2mL for full plate)\n Channel 3: MasterMix (20\u00b5L per sample, 2mL for full plate)\n Channel 4: Sample (30\u00b5L per sample, 3mL for full plate)\nSlot 5: Opentrons Tips\nSlot 6: Opentrons Tips", "internal": "arcis-test-multi", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/arcis-single-test/README.json b/protoBuilds/arcis-single-test/README.json index f51fc8cb6..7aa854d9a 100644 --- a/protoBuilds/arcis-single-test/README.json +++ b/protoBuilds/arcis-single-test/README.json @@ -5,7 +5,7 @@ "Arcis Blood Kit" ] }, - "description": "Note: This is an updated version (apiV1 to apiV2) of this protocol\nThis protocol is designed for running tests with the Arcis Blood Kit (further instructions about the protocol can be found here). With the Arcis Blood Kit, nucleic acid investigations can be performed easily and efficiently with the two included reagents. This protocol calls for the use of a P50-Single and P300-Single pipettes, as well as Opentrons Tube Racks, Corning 96-well, 360\u03bcL flat plate, and two Bioplastics 100\u03bcL plates.\n\n\n\nArcis Blood Kit\nOpentrons P50 Single Channel Pipette\nOpentrons P300 Single Channel Pipette\nOpentrons 50uL/300uL Tips\nOpentrons 4-in-1 Tube Rack Set\nCorning 96-Well Plate 360\u00b5L, Flat\nBioplastics 8-Tube Strip Mat, 100\u00b5L\n1.5mL Eppendorf Safe-Lock Tube\n15mL Conical Tube\n50mL Conical Tube\nSamples\n\n\n\nSlot 1: Opentrons Tiprack\nSlot 2: Corning 360\u00b5L Plate, clean and empty\nSlot 3: Bioplastics Plate (in holder), clean and empty\nSlot 4: Bioplastics Plate (in holder), clean and empty\nSlot 5: Opentrons 24 Tube Rack with 1.5mL Eppendorf Tubes\n* A1: Sample (1000\u00b5L)\n* A2: PCR Mastermix (1500\u00b5L)\nSlot 6: Opentrons 10 Tube Rack with Conical Tubes\n* A1: Reagent 2 (2000\u00b5L)\n* A3: Reagent 1 (10000\u00b5L)", + "description": "Note: This is an updated version (apiV1 to apiV2) of this protocol\nThis protocol is designed for running tests with the Arcis Blood Kit (further instructions about the protocol can be found here). With the Arcis Blood Kit, nucleic acid investigations can be performed easily and efficiently with the two included reagents. This protocol calls for the use of a P50-Single and P300-Single pipettes, as well as Opentrons Tube Racks, Corning 96-well, 360\u03bcL flat plate, and two Bioplastics 100\u03bcL plates.\n\n\n\nArcis Blood Kit\nOpentrons P50 Single Channel Pipette\nOpentrons P300 Single Channel Pipette\nOpentrons 50uL/300uL Tips\nOpentrons 4-in-1 Tube Rack Set\nCorning 96-Well Plate 360\u00b5L, Flat\nBioplastics 8-Tube Strip Mat, 100\u00b5L\n1.5mL Eppendorf Safe-Lock Tube\n15mL Conical Tube\n50mL Conical Tube\nSamples\n\n\n\nSlot 1: Opentrons Tiprack\nSlot 2: Corning 360\u00b5L Plate, clean and empty\nSlot 3: Bioplastics Plate (in holder), clean and empty\nSlot 4: Bioplastics Plate (in holder), clean and empty\nSlot 5: Opentrons 24 Tube Rack with 1.5mL Eppendorf Tubes\n A1: Sample (1000\u00b5L)\n A2: PCR Mastermix (1500\u00b5L)\nSlot 6: Opentrons 10 Tube Rack with Conical Tubes\n A1: Reagent 2 (2000\u00b5L)\n A3: Reagent 1 (10000\u00b5L)", "internal": "arcis-single-test", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/batch-test-plating/README.json b/protoBuilds/batch-test-plating/README.json index d5113133d..3faa070d8 100644 --- a/protoBuilds/batch-test-plating/README.json +++ b/protoBuilds/batch-test-plating/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "This is a flexible protocol that helps you to prepare the PCR plate for a batch test of 12 samples and 2 No Template Controls, with the previous adition of the Master Mix\nThe protocol is broken down into 3 main parts:\n* Mix dispensing\n* Samples Dispensing\n* NTC dispensing\n", + "description": "This is a flexible protocol that helps you to prepare the PCR plate for a batch test of 12 samples and 2 No Template Controls, with the previous adition of the Master Mix\nThe protocol is broken down into 3 main parts:\n Mix dispensing\n Samples Dispensing\n* NTC dispensing\n", "internal": "batch-test-plating", "labware": "\nnest_96_wellplate_100ul_pcr_full_skirt\nopentrons_96_filtertiprack_20ul\nopentrons_24_tuberack_generic_2ml_screwcap\n", "markdown": { diff --git a/protoBuilds/bc-rnadvance-viral-feat/README.json b/protoBuilds/bc-rnadvance-viral-feat/README.json index 45a04f4b0..ab52fa500 100644 --- a/protoBuilds/bc-rnadvance-viral-feat/README.json +++ b/protoBuilds/bc-rnadvance-viral-feat/README.json @@ -33,7 +33,7 @@ "pipettes": "\nOpentrons P300 8-Channel Electronic Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\nThis section should consist of a numerical outline of the protocol steps, somewhat analogous to the steps outlined by the user in their custom protocol submission.\nexample step: Samples are transferred from the source tuberacks on slots 1-2 to the PCR plate on slot 3, down columns and then across rows.\nexample step: Waste is removed from each sample on the magnetic module, ensuring the bead pellets are not contacted by the pipette tips.\n", - "reagent-setup": "\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n\nVolumes per reservoir channel: (for 96-sample run, not including dead volume):\n* 10mL of 100% Isopropanol + 250uL of bead BBD\n* 10mL of Wash WBE\n* 10mL of 70% Ethanol\n* 4mL of nuclease-free water\n", + "reagent-setup": "\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n\nVolumes per reservoir channel: (for 96-sample run, not including dead volume):\n 10mL of 100% Isopropanol + 250uL of bead BBD\n 10mL of Wash WBE\n 10mL of 70% Ethanol\n 4mL of nuclease-free water\n", "reagents": [ "Beckman Coulter RNAdvance Viral kit" ], diff --git a/protoBuilds/bc-rnadvance-viral/README.json b/protoBuilds/bc-rnadvance-viral/README.json index f5621e439..e360b538e 100644 --- a/protoBuilds/bc-rnadvance-viral/README.json +++ b/protoBuilds/bc-rnadvance-viral/README.json @@ -33,7 +33,7 @@ "partner": "Beckman Coulter Life Sciences", "pipettes": "\nOpentrons P300 8-Channel Electronic Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n\nVolumes per reservoir channel: (for 96-sample run, not including dead volume):\n* 10mL of 100% Isopropanol + 250uL of bead BBD\n* 10mL of Wash WBE\n* 10mL of 70% Ethanol\n* 4mL of nuclease-free water\n", + "reagent-setup": "\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n\nVolumes per reservoir channel: (for 96-sample run, not including dead volume):\n 10mL of 100% Isopropanol + 250uL of bead BBD\n 10mL of Wash WBE\n 10mL of 70% Ethanol\n 4mL of nuclease-free water\n", "reagents": [ "Beckman Coulter RNAdvance Viral kit" ], diff --git a/protoBuilds/bpg-rna-extraction/README.json b/protoBuilds/bpg-rna-extraction/README.json index 95ec2ac8f..c13c6c951 100644 --- a/protoBuilds/bpg-rna-extraction/README.json +++ b/protoBuilds/bpg-rna-extraction/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This protocol is currently being tested and is subject to change\nThis protocol automates the pureBASE RNA protocol by BP Genomics.\nAdditionally, it adds the 4ul of internal extraction control RNA as described in the 2019-nCoV Detection Assay protocol.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette\nOpentrons P1000 Single-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL or Opentrons 24 Tuberack with 2mL Tubes\nNEST Deep Well Plate, 1mL\nNEST 1-Well Reservoir, 195mL\n\n\n\nMay need to change pending revisions\nSlot 1: NEST 96-Well PCR Plate (for elutes)\nSlot 2: NEST 12-Well Reservoir, 15mL or Opentrons 24 Tuberack with 2mL Tubes, with Reagents\nIf using NEST 12-Well Reservoir, reagents should be loaded in the following configuration:\n* A1: Internal Extraction Control RNA\n* A2: Magbeads (in isopropanol; 20ul beads, 560ul isopropanol per sample)\n* A5: Wash Buffer 1\n* A7: Wash Buffer 2\n* A9: Ethanol\n* A10: Ethanol\n* A12: Nuclease-Free Water\nIf using Opentrons 24-Tuberack & 2mL Tubes, reagents should be loaded in the following configuration:\n* A1: Internal Exctraction Control RNA\n* A3: Magbeads (in isopropanol; 20ul beads, 560ul isopropanol per sample)\n* A5: Wash Buffer 1\n* C1: Wash Buffer 2\n* C3: Ethanol\n* C4: Ethanol\n* C6: Nuclease-Free Water\nSlot 3: Opentrons 20ul Filter Tips\nSlot 4: MagDeck, with Deep Well Plate containing 400ul of sample\nSlot 5: Reservoir for Liquid Waste\nSlot 6: Opentrons 1000ul Filter Tips\nUsing the customizations fields, below set up your protocol.\n* Number of Samples: Specify the number of samples you'd like to run.\n* P20 Single Mount: Specify which mount (left or right) the P20 Single is attached to.\n* P1000 Single Mount: Specify which mount (left or right) the P1000 Single is attached to.\n* Labware for Reagents: Specify which labware (NEST 12-Channel Reservoir or Opentrons 24-Tuberack) will house the reagents. This labware (& reagents) should be loaded in slot 2 and reagents should be loaded as described above.", + "description": "This protocol is currently being tested and is subject to change\nThis protocol automates the pureBASE RNA protocol by BP Genomics.\nAdditionally, it adds the 4ul of internal extraction control RNA as described in the 2019-nCoV Detection Assay protocol.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette\nOpentrons P1000 Single-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL or Opentrons 24 Tuberack with 2mL Tubes\nNEST Deep Well Plate, 1mL\nNEST 1-Well Reservoir, 195mL\n\n\n\nMay need to change pending revisions\nSlot 1: NEST 96-Well PCR Plate (for elutes)\nSlot 2: NEST 12-Well Reservoir, 15mL or Opentrons 24 Tuberack with 2mL Tubes, with Reagents\nIf using NEST 12-Well Reservoir, reagents should be loaded in the following configuration:\n A1: Internal Extraction Control RNA\n A2: Magbeads (in isopropanol; 20ul beads, 560ul isopropanol per sample)\n A5: Wash Buffer 1\n A7: Wash Buffer 2\n A9: Ethanol\n A10: Ethanol\n A12: Nuclease-Free Water\nIf using Opentrons 24-Tuberack & 2mL Tubes, reagents should be loaded in the following configuration:\n A1: Internal Exctraction Control RNA\n A3: Magbeads (in isopropanol; 20ul beads, 560ul isopropanol per sample)\n A5: Wash Buffer 1\n C1: Wash Buffer 2\n C3: Ethanol\n C4: Ethanol\n C6: Nuclease-Free Water\nSlot 3: Opentrons 20ul Filter Tips\nSlot 4: MagDeck, with Deep Well Plate containing 400ul of sample\nSlot 5: Reservoir for Liquid Waste\nSlot 6: Opentrons 1000ul Filter Tips\nUsing the customizations fields, below set up your protocol.\n Number of Samples: Specify the number of samples you'd like to run.\n P20 Single Mount: Specify which mount (left or right) the P20 Single is attached to.\n P1000 Single Mount: Specify which mount (left or right) the P1000 Single is attached to.\n Labware for Reagents: Specify which labware (NEST 12-Channel Reservoir or Opentrons 24-Tuberack) will house the reagents. This labware (& reagents) should be loaded in slot 2 and reagents should be loaded as described above.", "internal": "bpg-rna-extraction", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/cepheid/README.json b/protoBuilds/cepheid/README.json index 1b7f01a42..7f9bb5eb8 100644 --- a/protoBuilds/cepheid/README.json +++ b/protoBuilds/cepheid/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol automates the pooling of samples and distribution to Cepheid for rapid Covid-19 diagnostics.\nThe protocol begins by pooling samples in groups of 10. Once pooled, the pooled samples are mixed and transferred to the Cepheid device on a custom adapter containing the Cepheid device on the deck of the OT-2.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples to run (in groups of 10).\n* P1000 Mount: Specify which mount the P1000 Single-Channel Pipette (GEN2) is attached to\n", + "description": "This protocol automates the pooling of samples and distribution to Cepheid for rapid Covid-19 diagnostics.\nThe protocol begins by pooling samples in groups of 10. Once pooled, the pooled samples are mixed and transferred to the Cepheid device on a custom adapter containing the Cepheid device on the deck of the OT-2.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples to run (in groups of 10).\n P1000 Mount: Specify which mount the P1000 Single-Channel Pipette (GEN2) is attached to\n", "internal": "cepheid", "labware": "\nOpentrons 15-Tube Rack\n12mL Tubes\nCepheid\n", "markdown": { diff --git a/protoBuilds/checkit/README.json b/protoBuilds/checkit/README.json index 1165c078a..5dba19567 100644 --- a/protoBuilds/checkit/README.json +++ b/protoBuilds/checkit/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol performs Next Advance Checkit Go volume accuracy testing for Opentrons electronic pipettes on the OT-2. The user can select which model Checkit Go cartridge with which to test their pipette accuracy (5, 10, 20, or 50ul).\nThis protocol is meant to be used with the following Opentrons pipettes:\n* P20 Single-Channel\n* P20 8-Channel\n* P300 Single-Channel\n* P300 8-Channel\nCheckit Go devices are shipped with a red dye to use for testing, but you may also want to use their red dye pellets. Keep in mind, the protocol you find here is only tested with the Next Advance dye that is provided with the plates. If you plan to use the device with any other liquids, optimizations to the protocol will need to be made. Please contact Next advance support for questions about which liquids can be used on their devices. Contact Opentrons support with questions about the protocol.\n", + "description": "This protocol performs Next Advance Checkit Go volume accuracy testing for Opentrons electronic pipettes on the OT-2. The user can select which model Checkit Go cartridge with which to test their pipette accuracy (5, 10, 20, or 50ul).\nThis protocol is meant to be used with the following Opentrons pipettes:\n P20 Single-Channel\n P20 8-Channel\n P300 Single-Channel\n P300 8-Channel\nCheckit Go devices are shipped with a red dye to use for testing, but you may also want to use their red dye pellets. Keep in mind, the protocol you find here is only tested with the Next Advance dye that is provided with the plates. If you plan to use the device with any other liquids, optimizations to the protocol will need to be made. Please contact Next advance support for questions about which liquids can be used on their devices. Contact Opentrons support with questions about the protocol.\n", "internal": "checkit", "labware": "\nNext Advance Checkit Go Cartridge\nOpentrons 20/300ul Tiprack (depending on the pipette model used in the test)\n", "markdown": { diff --git a/protoBuilds/cherrypicking_simple/README.json b/protoBuilds/cherrypicking_simple/README.json index 4fe55c277..d75ac9654 100644 --- a/protoBuilds/cherrypicking_simple/README.json +++ b/protoBuilds/cherrypicking_simple/README.json @@ -5,7 +5,7 @@ "Cherrypicking" ] }, - "description": "\nCherrypicking, or hit-picking, is a key component of many workflows from high-throughput screening to microbial transfections. With this protocol, you can easily select specific wells in a 96 or 384 microwell plate without worrying about missing or selecting the wrong well. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nMicroplates (96-well or 384-well)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nTipracks should be loaded in Slot 1 (if using more than 96 tips, Slots 4, 7, and 10 can be loaded as well).\nThe Source Plate should be loaded in Slot 2. If using multiple Source Plates, Source Plates 1, 2, 3, and 4 should be loaded into Slot 2, Slot 5, Slot 8, and Slot 11, respectively.\nNote: If using multiple Source Plates, you must specify the Source Plate in the third column of the CSV (see below for examples)\nThe Destination Plate should be loaded in Slot 3.\nNote: The Destination Plate will receive each cherrypicking transfer sequentially, filling up the plate in well A1, then B1, etc.\nCSV Format\nYour cherrypicking transfers must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL).\n\nIn the first example, 40\u03bcL will be removed from well A3 in your source plate, and placed in well A1 in your destination plate. 36\u03bcL will be removed from well D4 in your source plate, and placed in well B1 in your destination plate.\n\nIn the second example, 100\u03bcL will be transferred from well E5 in \"Plate 1\" (slot 2) to well A1 in the destination plate (slot 3). After this, 100\u03bcL will be transferred from well G10 in \"Plate 3\" (slot 8) to well B1 in the destination plate (slot 3).\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV for use with this protocol.\nUsing the customizations fields, below set up your protocol.\n* Volumes CSV: Upload the .csv file containing your well locations, volumes, and source plate (optional).\n* Pipette Model: Select which pipette you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n* Source Plate Type: Select which (source) plate you will pick samples from.\n* Destination Plate Type: Select which (destination) plate you will dispense into.\n* Filter Tips: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", + "description": "\nCherrypicking, or hit-picking, is a key component of many workflows from high-throughput screening to microbial transfections. With this protocol, you can easily select specific wells in a 96 or 384 microwell plate without worrying about missing or selecting the wrong well. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nMicroplates (96-well or 384-well)\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nTipracks should be loaded in Slot 1 (if using more than 96 tips, Slots 4, 7, and 10 can be loaded as well).\nThe Source Plate should be loaded in Slot 2. If using multiple Source Plates, Source Plates 1, 2, 3, and 4 should be loaded into Slot 2, Slot 5, Slot 8, and Slot 11, respectively.\nNote: If using multiple Source Plates, you must specify the Source Plate in the third column of the CSV (see below for examples)\nThe Destination Plate should be loaded in Slot 3.\nNote: The Destination Plate will receive each cherrypicking transfer sequentially, filling up the plate in well A1, then B1, etc.\nCSV Format\nYour cherrypicking transfers must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL).\n\nIn the first example, 40\u03bcL will be removed from well A3 in your source plate, and placed in well A1 in your destination plate. 36\u03bcL will be removed from well D4 in your source plate, and placed in well B1 in your destination plate.\n\nIn the second example, 100\u03bcL will be transferred from well E5 in \"Plate 1\" (slot 2) to well A1 in the destination plate (slot 3). After this, 100\u03bcL will be transferred from well G10 in \"Plate 3\" (slot 8) to well B1 in the destination plate (slot 3).\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV for use with this protocol.\nUsing the customizations fields, below set up your protocol.\n Volumes CSV: Upload the .csv file containing your well locations, volumes, and source plate (optional).\n Pipette Model: Select which pipette you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n Source Plate Type: Select which (source) plate you will pick samples from.\n Destination Plate Type: Select which (destination) plate you will dispense into.\n Filter Tips: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", "internal": "cherrypicking_simple", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/complete-pcr/README.json b/protoBuilds/complete-pcr/README.json index dbeeb334f..6ba85f0a3 100644 --- a/protoBuilds/complete-pcr/README.json +++ b/protoBuilds/complete-pcr/README.json @@ -5,7 +5,7 @@ "Complete PCR Workflow" ] }, - "description": "Part 1 of 2: Master Mix Assembly\nLinks:\n* Part 1: Master Mix Assembly\n* Part 2: Master Mix Distribution and DNA Transfer\n* Part 3: Thermocycler\nThis protocol allows your robot to create a master mix solution using any reagents stored in a 2 mL Eppendorf tube rack or a 2 mL screwcap tube rack. The master mix will be created in well A1 of the trough. The ingredient information will be provided as a CSV file. See Additional Notes for more details.\n\nYou will need:\n* 4-in-1 Tube Rack Set\n* 12-well Trough", + "description": "Part 1 of 2: Master Mix Assembly\nLinks:\n Part 1: Master Mix Assembly\n Part 2: Master Mix Distribution and DNA Transfer\n* Part 3: Thermocycler\nThis protocol allows your robot to create a master mix solution using any reagents stored in a 2 mL Eppendorf tube rack or a 2 mL screwcap tube rack. The master mix will be created in well A1 of the trough. The ingredient information will be provided as a CSV file. See Additional Notes for more details.\n\nYou will need:\n 4-in-1 Tube Rack Set\n 12-well Trough", "internal": "OT-2 PCR Prep v2", "markdown": { "author": "[Opentrons](http://www.opentrons.com/)\n\n", diff --git a/protoBuilds/covid19-rna-extraction/README.json b/protoBuilds/covid19-rna-extraction/README.json index 97da4c652..f0d2ffcfa 100644 --- a/protoBuilds/covid19-rna-extraction/README.json +++ b/protoBuilds/covid19-rna-extraction/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This is a flexible protocol accommodating a wide range of commercial RNA extraction workflows for COVID-19 sample processing. The protocol is broken down into 5 main parts:\n* binding buffer addition to samples\n* bead wash 3x using magnetic module\n* final elution to chilled PCR plate\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nOpentrons temperature module\nNEST 12 Well Reservoir 15 mL or USA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nNEST 96 Deepwell Plate 2mL or USA Scientific 96 Deep Well Plate 2.4 mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 5\nReservoir 2: slot 2\n\n", + "description": "This is a flexible protocol accommodating a wide range of commercial RNA extraction workflows for COVID-19 sample processing. The protocol is broken down into 5 main parts:\n binding buffer addition to samples\n bead wash 3x using magnetic module\n* final elution to chilled PCR plate\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n\n \nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons magnetic module\nOpentrons temperature module\nNEST 12 Well Reservoir 15 mL or USA Scientific 12 Well Reservoir 22 mL\nNEST 1 Well Reservoir 195 mL\nNEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nNEST 96 Deepwell Plate 2mL or USA Scientific 96 Deep Well Plate 2.4 mL\nOpentrons 96 Filter Tip Rack 200 \u00b5L\n\n\n\n\nReservoir 1: slot 5\nReservoir 2: slot 2\n\n", "internal": "covid-19-rna-extraction", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/e54ada/README.json b/protoBuilds/e54ada/README.json index da2dfa2c2..cfa6118ce 100644 --- a/protoBuilds/e54ada/README.json +++ b/protoBuilds/e54ada/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nTube rack in slot 6 is only used when under 7 samples are specified. Beads are loaded in A1 of tube rack for 1-6 samples. If samples are 7-96 beads are loaded in slot 3, well 12\n\n", - "description": "This is a bead-based purification of nucleic acids using either BioRad 96 well plates or Grenier 96 well plates. Using P300 single and multi channel pipettes we have flexibility using 4-in-1 tube racks or 12 well reservoirs to hold beads. The beads can be diluted with 40% PEG 8000 mixtures or left neat from the reagent bottle.\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96)\n* Reaction Volume: Specify the starting sample volume in uL for the first plate\n* Bead Ratio: Specify the ratio of beads to sample volume with a float. Default is 1.8\n* Elution Volume: Specify the volume of elution liquid to use and subsequently transfer to the final plate in uL\n* P300 Multi Channel Pipette Mount: Specify which side the multi-channel P300 is mounted to. The single-channel P300 will default to the opposite side\n* Well Plate Type: Change between the BioRad plate in the OT-2 default labware library and the custom definition for Greiner 96 well plates with a circular well\n* Flash: Specify whether the robot will flash on pauses for tip rack refills and trash alerts\n", + "description": "This is a bead-based purification of nucleic acids using either BioRad 96 well plates or Grenier 96 well plates. Using P300 single and multi channel pipettes we have flexibility using 4-in-1 tube racks or 12 well reservoirs to hold beads. The beads can be diluted with 40% PEG 8000 mixtures or left neat from the reagent bottle.\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96)\n Reaction Volume: Specify the starting sample volume in uL for the first plate\n Bead Ratio: Specify the ratio of beads to sample volume with a float. Default is 1.8\n Elution Volume: Specify the volume of elution liquid to use and subsequently transfer to the final plate in uL\n P300 Multi Channel Pipette Mount: Specify which side the multi-channel P300 is mounted to. The single-channel P300 will default to the opposite side\n Well Plate Type: Change between the BioRad plate in the OT-2 default labware library and the custom definition for Greiner 96 well plates with a circular well\n* Flash: Specify whether the robot will flash on pauses for tip rack refills and trash alerts\n", "internal": "e54ada", "labware": "\nNEST 12 Reservoir 15mL\nOpentrons 200uL Filter Tips\nOpentrons 4-in-1 Tube Rack\nBioRad 96 Well Plate\nGreiner Microplate, 96 Well, PP, V-Bottom\n", "markdown": { diff --git a/protoBuilds/e54ada_rt/README.json b/protoBuilds/e54ada_rt/README.json index b010aa78c..a8afd3abb 100644 --- a/protoBuilds/e54ada_rt/README.json +++ b/protoBuilds/e54ada_rt/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nTube racks in slots 1, 2, 4, and 5 map directly to the 96 well plate. I.e. if 95 samples are specified all four tube racks will load in, RT mix will be in the bottom right well, C4, for slot 2. Well G12 will have primers added from slot 2, tube C3. If 13 samples are specified, the tube racks in slot 4 and 1 will load in, RT mix will be in well B2 in slot 1 (the 14th tube). Slot 1 A1's primer will add to well E1 in slot 3's well plate. Click here for an explanatory spreadsheet\n\n", - "description": "This is a plate filling protocol for a reverse transcriptase procedure. Up to 95 samples can be prepped using 4-in-1 tube racks filled with barcode primer mixes and a prepared enzyme mix in the final tube.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples this run (1-95)\n* Reagent Volume to Add: Specify the volume of RT mix to add. Default is 4.7 uL\n* Well Plate Type: Change between the BioRad plate in the OT-2 default labware library and the custom definition for Greiner 96 well plates with a circular well\n* P20 Mount: Specify which side the single-channel P20 is mounted to\n", + "description": "This is a plate filling protocol for a reverse transcriptase procedure. Up to 95 samples can be prepped using 4-in-1 tube racks filled with barcode primer mixes and a prepared enzyme mix in the final tube.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples this run (1-95)\n Reagent Volume to Add: Specify the volume of RT mix to add. Default is 4.7 uL\n Well Plate Type: Change between the BioRad plate in the OT-2 default labware library and the custom definition for Greiner 96 well plates with a circular well\n P20 Mount: Specify which side the single-channel P20 is mounted to\n", "internal": "e54ada", "labware": "\nOpentrons 20uL Filter Tips\nOpentrons 4-in-1 Tube Rack\nBioRad 96 Well Plate\nGreiner Microplate, 96 Well, PP, V-Bottom\n", "markdown": { diff --git a/protoBuilds/generic_ngs_prep/README.json b/protoBuilds/generic_ngs_prep/README.json index 8fdcc62f1..ea0991d7c 100644 --- a/protoBuilds/generic_ngs_prep/README.json +++ b/protoBuilds/generic_ngs_prep/README.json @@ -5,10 +5,10 @@ "Generic" ] }, - "deck-setup": "Note: The deck setup changes throughout the course of the protocol. The initial calibration layout may differ from the final setup. Please follow the initial calibration setup and any instructions during the pauses.\nInitial deck state:\n\nStep 1\n* Slot 1: Temperature Module slot 1 + Sample Plate\n* Slot 2: Reagent reservoir (SPRI, Buffer I, Mastermix)\n* Slot 3: Magnetic Module (Empty)\n* Slot 4: Temperature Module slot 4 + Reagent 1 Plate\n* Slot 6: 1 Well Reservoir (Ethanol)\n* Slot 7: Temperature Module slot 7 + Reagent 2 plate\n* Slot 8: Opentrons 200 uL Filter Tips\n* Slot 9: Opentrons 200 uL Filter Tips\n* Slot 10: Opentrons 20 uL Filter Tips\n* Slot 11: Opentrons 20 uL Filter Tips\nStep 2\n* Slot 1: Temperature Module slot 1\n* Slot 2: Reagent reservoir (SPRI, Buffer I, Mastermix)\n* Slot 3: Magnetic Module + Sample plate\n* Slot 4: Temperature Module slot 4 + Primers\n* Slot 6: 1 Well Reservoir (Ethanol Reservoir)\n* Slot 7: Temperature Module slot 7 + Indexing plate\n* Slot 8: Opentrons 200 uL Filter Tips\n* Slot 9: Opentrons 200 uL Filter Tips\n* Slot 10: Opentrons 20 uL Filter Tips\n* Slot 11: Opentrons 20 uL Filter Tips\n", - "description": "This protocol performs a generic NGS Library Prep. It utilizes up to three temperature modules in Slot 1, 4 and 7 for the cooling of reagents. It also utilizes the magnetic module for bead based purification of samples.\nExplanation of parameters below:\n* P20 Multichannel GEN2 Mount Position: Choose the mount position of the P20 Multichannel GEN2 pipette. (left or right)\n* P300 Multichannel GEN2 Mount Position: Choose the mount position of the P300 Multichannel GEN2 pipette. (left or right\n* Number of Samples: Enter total number of samples in the protocol run. Note: Because both pipettes are 8-channels, the number of samples should be a multiple of 8 or close if possible, otherwise it will use up additional tips for an entire column.\n* Temperature module in slot 1 (Optional parameter) Specify which temperature module to use in slot 1 (or None). This temperature module would allow the user to control the temperature of the sample plate in part 1 of the protocol.\n* Temperature module in slot 1 (Optional parameter) Specify which temperature module to use in slot 4 (or None). This temperature module would allow the user to control the temperature of reagent plate 1 in part 1 of the protocol, and the primer plate in part 2.\n* Temperature module in slot 7 (Optional parameter) Specify which temperature module to use in slot 7 (or None). This temperature module would allow the user to control the temperature of reagent plate 2 in part 1 of the protocol, and the Indexing plate in part 2.\n* Sample plate The sample plate holds DNA samples and is the site of mixing with buffers and reagents in part 1.\n* Reagent 1 plate The reagent 1 plate holds the first mixing reagent in column 1 (e.g. a buffer or an enzyme) to be mixed with the samples\n* Reagent 2 plate The reagent 2 plate holds the second mixing reagent in column 1 (e.g. a buffer or an enzyme) to be mixed with the samples.\n* Primer plate Contains primers to be mixed with DNA samples in step 2\n* Reagent reservoir The (12 well) reservoir contains paramagnetic bead solution, PCR buffer, and PCR mastermix.\n* Ethanol reservoir Ethanol solution for washing beads, e.g. 80:20 ethanol:water. Uses 180 \u00b5L per sample\n* Number of Samples The number of DNA samples (up to 96)\n* Temperature (deg C) for temperature module on slot x in part 1 These parameters for each of the temperature modules allow the user to set the temperatures for all/any temperature module in part 1.\n* Temperature (deg C) for temperature module on slot x in part 2 These parameters for each of the temperature modules allow the user to set the temperatures for all/any temperature module in part 2.\n* Volume of reagent 1 to add Volume of reagent 1 to add to samples, e.g. an enzyme or a reaction buffer\n* Volume of reagent 2 to add Volume of reagent 2 to add to samples, e.g. an enzyme or a reaction buffer\n* Ethanol wash volume The volume of ethanol solution to use for bead washing\n* Mastermix volume Volume of PCR mastermix for the PCR reaction in step 2, this is added to the indexing plate\n* Primer mix volume Volume of primer mix for the PCR reaction in step 2, this is added to the indexing plate\n* Bead volume Volume of paramagnetic bead solution to use for cleaning up the DNA from the enzymatic reaction in part 1 of the protocol\n* Elution buffer volume The volume of elution buffer to use for eluting the DNA after the ethanol cleanup\n* Sample volume The initial volume of DNA on the sample plate\n* DNA supernatant volume The volume of clean DNA to be transferred from the magnetic deck plate to the indexing plate to be used in the PCR reaction\n", + "deck-setup": "Note: The deck setup changes throughout the course of the protocol. The initial calibration layout may differ from the final setup. Please follow the initial calibration setup and any instructions during the pauses.\nInitial deck state:\n\nStep 1\n Slot 1: Temperature Module slot 1 + Sample Plate\n Slot 2: Reagent reservoir (SPRI, Buffer I, Mastermix)\n Slot 3: Magnetic Module (Empty)\n Slot 4: Temperature Module slot 4 + Reagent 1 Plate\n Slot 6: 1 Well Reservoir (Ethanol)\n Slot 7: Temperature Module slot 7 + Reagent 2 plate\n Slot 8: Opentrons 200 uL Filter Tips\n Slot 9: Opentrons 200 uL Filter Tips\n Slot 10: Opentrons 20 uL Filter Tips\n Slot 11: Opentrons 20 uL Filter Tips\nStep 2\n Slot 1: Temperature Module slot 1\n Slot 2: Reagent reservoir (SPRI, Buffer I, Mastermix)\n Slot 3: Magnetic Module + Sample plate\n Slot 4: Temperature Module slot 4 + Primers\n Slot 6: 1 Well Reservoir (Ethanol Reservoir)\n Slot 7: Temperature Module slot 7 + Indexing plate\n Slot 8: Opentrons 200 uL Filter Tips\n Slot 9: Opentrons 200 uL Filter Tips\n Slot 10: Opentrons 20 uL Filter Tips\n Slot 11: Opentrons 20 uL Filter Tips\n", + "description": "This protocol performs a generic NGS Library Prep. It utilizes up to three temperature modules in Slot 1, 4 and 7 for the cooling of reagents. It also utilizes the magnetic module for bead based purification of samples.\nExplanation of parameters below:\n P20 Multichannel GEN2 Mount Position: Choose the mount position of the P20 Multichannel GEN2 pipette. (left or right)\n P300 Multichannel GEN2 Mount Position: Choose the mount position of the P300 Multichannel GEN2 pipette. (left or right\n Number of Samples: Enter total number of samples in the protocol run. Note: Because both pipettes are 8-channels, the number of samples should be a multiple of 8 or close if possible, otherwise it will use up additional tips for an entire column.\n Temperature module in slot 1 (Optional parameter) Specify which temperature module to use in slot 1 (or None). This temperature module would allow the user to control the temperature of the sample plate in part 1 of the protocol.\n Temperature module in slot 1 (Optional parameter) Specify which temperature module to use in slot 4 (or None). This temperature module would allow the user to control the temperature of reagent plate 1 in part 1 of the protocol, and the primer plate in part 2.\n Temperature module in slot 7 (Optional parameter) Specify which temperature module to use in slot 7 (or None). This temperature module would allow the user to control the temperature of reagent plate 2 in part 1 of the protocol, and the Indexing plate in part 2.\n Sample plate The sample plate holds DNA samples and is the site of mixing with buffers and reagents in part 1.\n Reagent 1 plate The reagent 1 plate holds the first mixing reagent in column 1 (e.g. a buffer or an enzyme) to be mixed with the samples\n Reagent 2 plate The reagent 2 plate holds the second mixing reagent in column 1 (e.g. a buffer or an enzyme) to be mixed with the samples.\n Primer plate Contains primers to be mixed with DNA samples in step 2\n Reagent reservoir The (12 well) reservoir contains paramagnetic bead solution, PCR buffer, and PCR mastermix.\n Ethanol reservoir Ethanol solution for washing beads, e.g. 80:20 ethanol:water. Uses 180 \u00b5L per sample\n Number of Samples The number of DNA samples (up to 96)\n Temperature (deg C) for temperature module on slot x in part 1 These parameters for each of the temperature modules allow the user to set the temperatures for all/any temperature module in part 1.\n Temperature (deg C) for temperature module on slot x in part 2 These parameters for each of the temperature modules allow the user to set the temperatures for all/any temperature module in part 2.\n Volume of reagent 1 to add Volume of reagent 1 to add to samples, e.g. an enzyme or a reaction buffer\n Volume of reagent 2 to add Volume of reagent 2 to add to samples, e.g. an enzyme or a reaction buffer\n Ethanol wash volume The volume of ethanol solution to use for bead washing\n Mastermix volume Volume of PCR mastermix for the PCR reaction in step 2, this is added to the indexing plate\n Primer mix volume Volume of primer mix for the PCR reaction in step 2, this is added to the indexing plate\n Bead volume Volume of paramagnetic bead solution to use for cleaning up the DNA from the enzymatic reaction in part 1 of the protocol\n Elution buffer volume The volume of elution buffer to use for eluting the DNA after the ethanol cleanup\n Sample volume The initial volume of DNA on the sample plate\n DNA supernatant volume The volume of clean DNA to be transferred from the magnetic deck plate to the indexing plate to be used in the PCR reaction\n", "internal": "generic_ngs_prep", - "labware": "Plates\n* Bio-Rad 96 Well Plate 200 \u00b5L PCR\n* Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\n* Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L\n* Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L\n* NEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nTips\n* Opentrons 96 Filter Tip Rack 200 \u00b5L\n* Opentrons 96 Filter Tip Rack 20 \u00b5L\n12 well reservoir options\n* NEST 12 Well Reservoir 15 mL\n* USA Scientific 12 Well Reservoir 22 mL\nreservoir options\n* Agilent 1 Well Reservoir 290 mL\n* Axygen 1 Well Reservoir 90 mL\n* NEST 1 Well Reservoir 195 mL\nPipettes\n* P20 Multichannel GEN2 Pipette\n* P300 Multichannel GEN2 Pipette\n", + "labware": "Plates\n Bio-Rad 96 Well Plate 200 \u00b5L PCR\n Opentrons 96 Well Aluminum Block with Generic PCR Strip 200 \u00b5L\n Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L\n Opentrons 96 Well Aluminum Block with NEST Well Plate 100 \u00b5L\n* NEST 96 Well Plate 100 \u00b5L PCR Full Skirt\nTips\n Opentrons 96 Filter Tip Rack 200 \u00b5L\n Opentrons 96 Filter Tip Rack 20 \u00b5L\n12 well reservoir options\n NEST 12 Well Reservoir 15 mL\n USA Scientific 12 Well Reservoir 22 mL\nreservoir options\n Agilent 1 Well Reservoir 290 mL\n Axygen 1 Well Reservoir 90 mL\n* NEST 1 Well Reservoir 195 mL\nPipettes\n P20 Multichannel GEN2 Pipette\n P300 Multichannel GEN2 Pipette\n", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", "categories": "* NGS Library Prep\n\t* Generic\n\n", diff --git a/protoBuilds/generic_pcr_prep_1/README.json b/protoBuilds/generic_pcr_prep_1/README.json index 9bd02e86d..0fd383e42 100644 --- a/protoBuilds/generic_pcr_prep_1/README.json +++ b/protoBuilds/generic_pcr_prep_1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nExample setup\n\n\n\n\nSlot 1: Tube rack or well plate 1\nSlot 2: Tube rack or well plate 2\nSlot 3: 12-Channel reservoir: Well 1 - Mastermix target\nSlot 4: Tiprack for the left pipette\nSlot 5: Tiprack for the right pipette\nSlot 6: Empty\nSlot 7: Empty\nSlot 8: Empty\nSlot 9: Empty\nSlot 10: Empty\nSlot 11: Empty\n\n", - "description": "Part 1 of 2: Master Mix Assembly\nThis protocol allows your robot to create a master mix solution using any reagents stored in one to three different pieces of labware such as a tube racks, well plates, and 12 well reservoirs. The master mix will be created in well A1 of the trough of the chosen reservoir. The ingredient information will be provided as a CSV file. See Additional Notes for more details.\nLinks:\n* Part 1: Master Mix Assembly\n* Part 2: Master Mix Distribution and DNA Transfer\nExplanation of parameters below:\n* right pipette type: Pipette for the right mount\n* Left pipette type: Pipette for the left mount\nFor the pipette choices it is important that the pipettes selected will cover the range of volumes used in the protocol\n* master mix .csv file: Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\n\n* Left pipette: Filter or regular tips? Select whether you want unfiltered or filtered tips. The protocol will load the appropriate tips, e.g. 20 uL tips for a 20 uL pipette, 1000 uL filtered/nonfiltered for a 1000 uL pipette etc.\n* Right pipette: Filter or regular tips? Select whether you want unfiltered or filtered tips. The protocol will load the appropriate tips, e.g. 20 uL tips for a 20 uL pipette, 1000 uL filtered/nonfiltered for a 1000 uL pipette etc.\n* Reagent labware 1 Choose the appropriate labware (such as tube racks or well plates) for your reagents, you may choose aluminum blocks if you intend to use a temperature module. This is referred to as \"slot 1\" in the .csv\n* Reagent labware 2 (Optional) Choose a secondary unit of labware for your reagents, you may choose aluminum blocks if you intend to use a temperature module. This is referred to as \"slot 2\" in the .csv\n* Twelve well Reservoir and mastermix destination Select the type of 12 well reservoir to use. The mastermix will be created in well A1. You may use the other wells as sources for reagents (slot 3 in the .csv)\n\n", + "description": "Part 1 of 2: Master Mix Assembly\nThis protocol allows your robot to create a master mix solution using any reagents stored in one to three different pieces of labware such as a tube racks, well plates, and 12 well reservoirs. The master mix will be created in well A1 of the trough of the chosen reservoir. The ingredient information will be provided as a CSV file. See Additional Notes for more details.\nLinks:\n Part 1: Master Mix Assembly\n Part 2: Master Mix Distribution and DNA Transfer\nExplanation of parameters below:\n right pipette type: Pipette for the right mount\n Left pipette type: Pipette for the left mount\nFor the pipette choices it is important that the pipettes selected will cover the range of volumes used in the protocol\n* master mix .csv file: Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\n\n Left pipette: Filter or regular tips? Select whether you want unfiltered or filtered tips. The protocol will load the appropriate tips, e.g. 20 uL tips for a 20 uL pipette, 1000 uL filtered/nonfiltered for a 1000 uL pipette etc.\n Right pipette: Filter or regular tips? Select whether you want unfiltered or filtered tips. The protocol will load the appropriate tips, e.g. 20 uL tips for a 20 uL pipette, 1000 uL filtered/nonfiltered for a 1000 uL pipette etc.\n Reagent labware 1 Choose the appropriate labware (such as tube racks or well plates) for your reagents, you may choose aluminum blocks if you intend to use a temperature module. This is referred to as \"slot 1\" in the .csv\n Reagent labware 2 (Optional) Choose a secondary unit of labware for your reagents, you may choose aluminum blocks if you intend to use a temperature module. This is referred to as \"slot 2\" in the .csv\n* Twelve well Reservoir and mastermix destination Select the type of 12 well reservoir to use. The mastermix will be created in well A1. You may use the other wells as sources for reagents (slot 3 in the .csv)\n\n", "internal": "generic_pcr_prep_1", "labware": "\nTube racks\nAluminum blocks\n12 well reservoirs\n", "markdown": { diff --git a/protoBuilds/generic_pcr_prep_2/README.json b/protoBuilds/generic_pcr_prep_2/README.json index 16579e860..10053de1c 100644 --- a/protoBuilds/generic_pcr_prep_2/README.json +++ b/protoBuilds/generic_pcr_prep_2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nExample setup with a 384 well destination plate and four 96 well plates\n\n\n\n\nSlot 1: Template DNA plate 2 (optional: for transferring to a 384 well plate)\nSlot 2: Template DNA plate 3 (optional: for transferring to a 384 well plate)\nSlot 3: Reservoir: or Deep well plate: Well 1 (to 8)- Mastermix source\nSlot 4: Tiprack 1 for the left pipette\nSlot 5: Tiprack 1 for the right pipette\nSlot 6: Destination plate (where mastermix and template DNA is combined, optionally on a temperature module)\nSlot 7: Tiprack 2 for the right pipette\nSlot 8: Tiprack 2 for the left pipette\nSlot 9: Template DNA plate 1 (optionally on a temperature module)\nSlot 10: Tiprack 3 for the left pipette\nSlot 11: Template DNA plate 4 (optional: for transferring to a 384 well plate)\n", - "description": "Part 2 of 2: Master Mix Distribution and DNA Transfer\nLinks:\n* Part 1: Master Mix Assembly\n* Part 2: Master Mix Distribution and DNA Transfer\nThis protocol allows your robot to distribute a master mix solution from well A1 of a reservoir or deep well plate to a target (a plate or a set of PCR strips on an aluminum block). The robot will then transfer DNA samples to the destination. At this point the samples can be mixed if so desired. The protocol works with both single- and multi-channel pipettes, just be sure that the minimum end of their combined volume range covers the smallest volume. There is also an option to place the DNA template plate, and the target plate on temperature modules. The protocol allows a user to 1) transfer the DNA samples of a 96 well plate to the target 96 well plate or 2) transfer up to four 96 well plates containing template DNA to a 384 well plate.\nIf only one pipette is selected it can use all 5 tipracks located on slots 4, 5, 7, 8, and 10. If two pipettes are loaded 4,7, and 10 are used by the left pipette and 5, and 8 by the right pipette.\nWhen 96 well plates are transferred with a multi-channel pipette to 384 well plates their columns are intercalated on the 384 well plate, e.g. column 1 and 2 of the 96 well plate go into odd the and even rows of the 1st column of the 384 well plate respectively. Then column 3, and 4 of the 96 well plate go into the next column of the 384 well plate etc.\nIf a single channel pipette is used the DNA will be transferred sequentially from 96 well plates to the 384 well plate\nExplanation of parameters below:\n* Number of samples : The number of DNA template samples to mix with PCR mastermix on the target well plate. This parameter controls how many plate columns the mastermix is transferred to as well as how many columns of samples are transferred to the destination plate.\n* Number of mixes: How many times to mix the DNA template samples with the mastermix after adding them together\n* Aspiration rate multiplier: A multiplier for controlling the flow rate of aspiration: Less than 1 to slow down, or greater than one to speed up aspiration.\n* Dispensation rate multiplier: A multiplier for controlling the flow rate of dispensation, less than 1 to slow down, or greater than one to speed up dispensation.\n* Right pipette type: Pipette in the right mount, it can be either a single channel or a multi-channel pipette\n* Left pipette type: Pipette in the left mount, it can be either a single channel or a multi-channel pipette.\n* Filtered or unfiltered tips for the left pipette?: Whether the left pipette is using filter or regular tips. for P20s and P10s the options are Opentrons 20 \u00b5L filtered tips, or 20 \u00b5L unfiltered.\nfor P50 and P300s the filtered tips are 200 \u00b5L Opentrons filtered tips, and the non-filtered are 300 \u00b5L Opentrons regular tips. For the P1000 the options is either Opentrons 1000 \u00b5L filtered or non-filtered tips.\n* Filtered or unfiltered tips for the right pipette?: Whether the right pipette is using filter or regular Opentrons tips\n* Mastermix volume (in \u00b5l): The volume of mastermix to transfer to each well on the destination plate (in \u00b5L)\n* DNA volume (in \u00b5l): The amount of DNA template to transfer to each destination plate from the DNA template plate (in \u00b5L)\n* Mastermix reservoir: A 1 well, or 12 well reservoir, or a deep well plate containing your PCR mastermix in well A1 (or the column spanning A1 to H1)\n* PCR well plate (or PCR strips) containing template DNA: Your source of template DNA, such as a 96 well plate (up to 4 when the destination plate is a 384 well plate)\n* Destination PCR well plate or PCR strips: This is the well plate where the PCR mastermix and the DNA template is transferred to and mixed. This can be a 96 well plate, PCR strips on an aluminum block, or a 384 well plate.\n* Temperature module for the 1st DNA template well plate: (Optional) You can load a temperature module for your (1st) DNA template well plate if you want to control its temperature.\n* Temperature module for the destination well plate: (Optional) You can load a temperature module for your destination well plate if you want to control its temperature.\n\n", + "description": "Part 2 of 2: Master Mix Distribution and DNA Transfer\nLinks:\n Part 1: Master Mix Assembly\n Part 2: Master Mix Distribution and DNA Transfer\nThis protocol allows your robot to distribute a master mix solution from well A1 of a reservoir or deep well plate to a target (a plate or a set of PCR strips on an aluminum block). The robot will then transfer DNA samples to the destination. At this point the samples can be mixed if so desired. The protocol works with both single- and multi-channel pipettes, just be sure that the minimum end of their combined volume range covers the smallest volume. There is also an option to place the DNA template plate, and the target plate on temperature modules. The protocol allows a user to 1) transfer the DNA samples of a 96 well plate to the target 96 well plate or 2) transfer up to four 96 well plates containing template DNA to a 384 well plate.\nIf only one pipette is selected it can use all 5 tipracks located on slots 4, 5, 7, 8, and 10. If two pipettes are loaded 4,7, and 10 are used by the left pipette and 5, and 8 by the right pipette.\nWhen 96 well plates are transferred with a multi-channel pipette to 384 well plates their columns are intercalated on the 384 well plate, e.g. column 1 and 2 of the 96 well plate go into odd the and even rows of the 1st column of the 384 well plate respectively. Then column 3, and 4 of the 96 well plate go into the next column of the 384 well plate etc.\nIf a single channel pipette is used the DNA will be transferred sequentially from 96 well plates to the 384 well plate\nExplanation of parameters below:\n Number of samples : The number of DNA template samples to mix with PCR mastermix on the target well plate. This parameter controls how many plate columns the mastermix is transferred to as well as how many columns of samples are transferred to the destination plate.\n Number of mixes: How many times to mix the DNA template samples with the mastermix after adding them together\n Aspiration rate multiplier: A multiplier for controlling the flow rate of aspiration: Less than 1 to slow down, or greater than one to speed up aspiration.\n Dispensation rate multiplier: A multiplier for controlling the flow rate of dispensation, less than 1 to slow down, or greater than one to speed up dispensation.\n Right pipette type: Pipette in the right mount, it can be either a single channel or a multi-channel pipette\n Left pipette type: Pipette in the left mount, it can be either a single channel or a multi-channel pipette.\n Filtered or unfiltered tips for the left pipette?: Whether the left pipette is using filter or regular tips. for P20s and P10s the options are Opentrons 20 \u00b5L filtered tips, or 20 \u00b5L unfiltered.\nfor P50 and P300s the filtered tips are 200 \u00b5L Opentrons filtered tips, and the non-filtered are 300 \u00b5L Opentrons regular tips. For the P1000 the options is either Opentrons 1000 \u00b5L filtered or non-filtered tips.\n Filtered or unfiltered tips for the right pipette?: Whether the right pipette is using filter or regular Opentrons tips\n Mastermix volume (in \u00b5l): The volume of mastermix to transfer to each well on the destination plate (in \u00b5L)\n DNA volume (in \u00b5l): The amount of DNA template to transfer to each destination plate from the DNA template plate (in \u00b5L)\n Mastermix reservoir: A 1 well, or 12 well reservoir, or a deep well plate containing your PCR mastermix in well A1 (or the column spanning A1 to H1)\n PCR well plate (or PCR strips) containing template DNA: Your source of template DNA, such as a 96 well plate (up to 4 when the destination plate is a 384 well plate)\n Destination PCR well plate or PCR strips: This is the well plate where the PCR mastermix and the DNA template is transferred to and mixed. This can be a 96 well plate, PCR strips on an aluminum block, or a 384 well plate.\n Temperature module for the 1st DNA template well plate: (Optional) You can load a temperature module for your (1st) DNA template well plate if you want to control its temperature.\n* Temperature module for the destination well plate: (Optional) You can load a temperature module for your destination well plate if you want to control its temperature.\n\n", "internal": "generic_pcr_prep_2", "labware": "\nReservoirs\nDeep Well plates which may also be used as mastermix reservoirs\nWell plates\nAlternatively: Well plate/PCR strips on aluminum blocks\n", "markdown": { diff --git a/protoBuilds/generic_station_A/README.json b/protoBuilds/generic_station_A/README.json index a0a9a7f77..492f4f1c2 100644 --- a/protoBuilds/generic_station_A/README.json +++ b/protoBuilds/generic_station_A/README.json @@ -5,7 +5,7 @@ "Sample Plating" ] }, - "description": "This protocol automates sample plating from collection tubes to a 96-well plate. After sample plating (Station A), the plate containing samples can be used on Station B for RNA extraction as outlined in our article on automating Covid-19 testing.\n\nUsing a Single-Channel Pipette, this protocol will transfer the user-specified volume from sample tubes placed in the Opentrons Tube Rack into a 96-well plate. Users can specify which pipette, the type of source tube, the type of destination plate, the number of samples to transfer, and the volume of each sample being transferred.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Single-Channel Pipette\nOpentrons Filter Tips\nOpentrons 4-in-1 Tube Rack Set\n96-Well Plate\nSample Tubes\n\n\n\nThe Opentrons tiprack should be placed in slot 3 and the 96-well plate should be placed in slot 2.\nWith this protocol, the Opentrons tube rack with samples will be accessed in the following order: slot 1, 4, 7, 10, 5, 8, 11 -- see below for examples.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify the number of samples to run (1-96)\n* Volume of Samples (in \u00b5L): Specify the volume to be transferred from sample tubes to destination plate (this volume should fall in the range of the selected pipette)\n* Destination Plate Labware: Specify whether to use the NEST Deepwell Plate, 2mL or the NEST PCR Plate as the destination plate\n* Source Tube Labware: Specify whether to use the Opentrons Tubebrack (24) with 2mL, 1.5mL, or 0.5mL tubes or the Opentrons Tuberack (15) with 15mL conical tubes.\n* Pipette Type: Specify which pipette (p300/p1000 GEN1/GEN2) to use (should be mounted on the right gantry)\n\n\nExample layout: 15 samples with 2mL tubes\n\n\n\nExample layout: 15 samples with 15mL tubes\n\n\n\nExample layout: 96 samples with 2mL tubes\n\n\n\nExample layout: 96 samples with 15mL tubes\n\n\n", + "description": "This protocol automates sample plating from collection tubes to a 96-well plate. After sample plating (Station A), the plate containing samples can be used on Station B for RNA extraction as outlined in our article on automating Covid-19 testing.\n\nUsing a Single-Channel Pipette, this protocol will transfer the user-specified volume from sample tubes placed in the Opentrons Tube Rack into a 96-well plate. Users can specify which pipette, the type of source tube, the type of destination plate, the number of samples to transfer, and the volume of each sample being transferred.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Single-Channel Pipette\nOpentrons Filter Tips\nOpentrons 4-in-1 Tube Rack Set\n96-Well Plate\nSample Tubes\n\n\n\nThe Opentrons tiprack should be placed in slot 3 and the 96-well plate should be placed in slot 2.\nWith this protocol, the Opentrons tube rack with samples will be accessed in the following order: slot 1, 4, 7, 10, 5, 8, 11 -- see below for examples.\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify the number of samples to run (1-96)\n Volume of Samples (in \u00b5L): Specify the volume to be transferred from sample tubes to destination plate (this volume should fall in the range of the selected pipette)\n Destination Plate Labware: Specify whether to use the NEST Deepwell Plate, 2mL or the NEST PCR Plate as the destination plate\n Source Tube Labware: Specify whether to use the Opentrons Tubebrack (24) with 2mL, 1.5mL, or 0.5mL tubes or the Opentrons Tuberack (15) with 15mL conical tubes.\n* Pipette Type: Specify which pipette (p300/p1000 GEN1/GEN2) to use (should be mounted on the right gantry)\n\n\nExample layout: 15 samples with 2mL tubes\n\n\n\nExample layout: 15 samples with 15mL tubes\n\n\n\nExample layout: 96 samples with 2mL tubes\n\n\n\nExample layout: 96 samples with 15mL tubes\n\n\n", "internal": "generic_station_A", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/generic_station_C/README.json b/protoBuilds/generic_station_C/README.json index 54886302f..63b7a26db 100644 --- a/protoBuilds/generic_station_C/README.json +++ b/protoBuilds/generic_station_C/README.json @@ -5,7 +5,7 @@ "qPCR Setup" ] }, - "description": "This protocol automates setting up a plate for (reverse transcriptase) qPCR. Using the purified nucleic acid samples from Station B (RNA Extraction), the samples are then aliquoted and mixed with the reaction mix of the assay as outlined in our article on automating Covid-19 testing.\n\nUsing a Single-Channel Pipette, this protocol will begin by transferring reaction mix (combination of master mix and primers/probes) from a 1.5mL tube in the 24-well aluminum block to the specified wells of a plate for qPCR. Then, using the Single-Channel Pipette or optional Multi-Channel Pipette, samples will be transferred from their plate to the qPCR plate and mixed with the reaction mix.\n\nThis protocol uses a custom labware definition. For more information on using labware with the OT-2, please see this support article.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Temperature Module with Aluminum Block Set)\nOpentrons Single-Channel Pipette\nOpentrons Multi-Channel Pipette, optional\nOpentrons Filter Tips\nNEST PCR Plate containing purified nucleic acid samples\nNEST 1.5mL Microcentrifuge Tube containing reaction mix(es)\nOptical 96-Well qPCR Plate\n\n\n\nThe Opentrons Temperature Module should be placed in slot 4 with the 96-Well Aluminum Block and qPCR plate on top. The temperature module can be pre-cooled through the Opentrons OT-2 Run App\n\nThe reaction mix(es) (master mix/primers/probes/etc) should kept in the microcentrifuge tube and placed in the 24-Well Aluminum Block (which can be put in the freezer beforehand to keep reagents cold) in slot 5. Up to three different reaction mixes can be used per plate and should be loaded in A1, B1, and C1.\n\nThe NEST PCR Plate containing purified nucleic acid samples should be placed in slot 1. The samples should be filled in column order (ie, 3 samples would go in wells A1, B1, and C1).\n\nThe Opentrons Tiprack for the Opentrons Single-Channel Pipette should be placed in slot 6.\n\nIf also using an Opentrons Multi-Channel Pipette that is the same volumetrically as the single-channel pipette and the total number of tips that will be used is less than 96, then the same tiprack in slot 6 can be utilized. Otherwise, another tiprack should be placed in slot 3.\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Specify the number of samples to run. If using more than one reaction mix, the number of samples would be the same for each reaction mix. If using 1 reaction mix, the maximum number of samples would be 96; if using 2 reaction mixes, the maximum would be 48; and if using 3 reaction mixes, the maxium is 32.\n* Number of Reaction Mixes: Select the number of reaction mixes (1, 2, or 3) that will be used.\n* Volume of Reaction Mix (\u00b5L): Specify the volume of the reaction mix(es) that should be added to each well of the qPCR plate.\n* Volume of Sample (\u00b5L): Specify the volume of the sample that should be transferred to each well of the qPCR plate.\n* Single-Channel Pipette Type (right mount): Select which single-channel pipette (p10, p50, or p20) that will be used. This pipette should be mounted to the right mount.\n* Multi-Channel Pipette Type (left mount): Select which multi-channel pipette (p10, p50, or p20) that will be used, if using (can also select none).\n\n\nExample layout: 48 samples with 2 reaction mixes\nnote: this configuration requires 98 tips, thus two tipracks are needed\n\n\n\nExample layout: 48 samples with 1 reaction mix and different pipettes\n\n\n", + "description": "This protocol automates setting up a plate for (reverse transcriptase) qPCR. Using the purified nucleic acid samples from Station B (RNA Extraction), the samples are then aliquoted and mixed with the reaction mix of the assay as outlined in our article on automating Covid-19 testing.\n\nUsing a Single-Channel Pipette, this protocol will begin by transferring reaction mix (combination of master mix and primers/probes) from a 1.5mL tube in the 24-well aluminum block to the specified wells of a plate for qPCR. Then, using the Single-Channel Pipette or optional Multi-Channel Pipette, samples will be transferred from their plate to the qPCR plate and mixed with the reaction mix.\n\nThis protocol uses a custom labware definition. For more information on using labware with the OT-2, please see this support article.\n\nIf you have any questions about this protocol, please email our Applications Engineering team at protocols@opentrons.com.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Temperature Module with Aluminum Block Set)\nOpentrons Single-Channel Pipette\nOpentrons Multi-Channel Pipette, optional\nOpentrons Filter Tips\nNEST PCR Plate containing purified nucleic acid samples\nNEST 1.5mL Microcentrifuge Tube containing reaction mix(es)\nOptical 96-Well qPCR Plate\n\n\n\nThe Opentrons Temperature Module should be placed in slot 4 with the 96-Well Aluminum Block and qPCR plate on top. The temperature module can be pre-cooled through the Opentrons OT-2 Run App\n\nThe reaction mix(es) (master mix/primers/probes/etc) should kept in the microcentrifuge tube and placed in the 24-Well Aluminum Block (which can be put in the freezer beforehand to keep reagents cold) in slot 5. Up to three different reaction mixes can be used per plate and should be loaded in A1, B1, and C1.\n\nThe NEST PCR Plate containing purified nucleic acid samples should be placed in slot 1. The samples should be filled in column order (ie, 3 samples would go in wells A1, B1, and C1).\n\nThe Opentrons Tiprack for the Opentrons Single-Channel Pipette should be placed in slot 6.\n\nIf also using an Opentrons Multi-Channel Pipette that is the same volumetrically as the single-channel pipette and the total number of tips that will be used is less than 96, then the same tiprack in slot 6 can be utilized. Otherwise, another tiprack should be placed in slot 3.\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Specify the number of samples to run. If using more than one reaction mix, the number of samples would be the same for each reaction mix. If using 1 reaction mix, the maximum number of samples would be 96; if using 2 reaction mixes, the maximum would be 48; and if using 3 reaction mixes, the maxium is 32.\n Number of Reaction Mixes: Select the number of reaction mixes (1, 2, or 3) that will be used.\n Volume of Reaction Mix (\u00b5L): Specify the volume of the reaction mix(es) that should be added to each well of the qPCR plate.\n Volume of Sample (\u00b5L): Specify the volume of the sample that should be transferred to each well of the qPCR plate.\n Single-Channel Pipette Type (right mount): Select which single-channel pipette (p10, p50, or p20) that will be used. This pipette should be mounted to the right mount.\n Multi-Channel Pipette Type (left mount): Select which multi-channel pipette (p10, p50, or p20) that will be used, if using (can also select none).\n\n\nExample layout: 48 samples with 2 reaction mixes\nnote: this configuration requires 98 tips, thus two tipracks are needed\n\n\n\nExample layout: 48 samples with 1 reaction mix and different pipettes\n\n\n", "internal": "generic_station_A", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/gna_octea/README.json b/protoBuilds/gna_octea/README.json index e97f1a4bb..a16fd60dd 100644 --- a/protoBuilds/gna_octea/README.json +++ b/protoBuilds/gna_octea/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates GNA Octea prep. Using the P300 Multi-Channel Pipette (GEN2) and the P300 Single-Channel Pipette (GEN2), all the reagents necessary for the sample prep are transferred to the samples and the samples are incubated on the Temperature Module and Magnetic Module. Once all sample prep has been completed, the samples are transferred to a custom plate containing the labware needed to test the samples on the GNA analyzer.\nThis protocol is still a work in progress and will be updated.\nUpdate (06/07/2021): This protocol has been updated per conversation and has several modifications (slight), such as, changing the distribution of reagent to multi-dispense and allowing the temperature module to heat up while pipetting occurs.\nUpdate (06/10/2021): This protocol has been updated and now includes new mixing functions and incorporated air gaps.\nExplanation of complex parameters below:\n* P300-Multi Mount: Select which mount the P300 Multi-Channel Pipette (GEN2) is attached to.\n* P300-Single Mount: Select which mount the P300 Single-Channel Pipette (GEN2) is attached to.\n* Number of Samples: Specify the number of samples to be run. Currently, 8 is the only number allowed.\n", + "description": "This protocol automates GNA Octea prep. Using the P300 Multi-Channel Pipette (GEN2) and the P300 Single-Channel Pipette (GEN2), all the reagents necessary for the sample prep are transferred to the samples and the samples are incubated on the Temperature Module and Magnetic Module. Once all sample prep has been completed, the samples are transferred to a custom plate containing the labware needed to test the samples on the GNA analyzer.\nThis protocol is still a work in progress and will be updated.\nUpdate (06/07/2021): This protocol has been updated per conversation and has several modifications (slight), such as, changing the distribution of reagent to multi-dispense and allowing the temperature module to heat up while pipetting occurs.\nUpdate (06/10/2021): This protocol has been updated and now includes new mixing functions and incorporated air gaps.\nExplanation of complex parameters below:\n P300-Multi Mount: Select which mount the P300 Multi-Channel Pipette (GEN2) is attached to.\n P300-Single Mount: Select which mount the P300 Single-Channel Pipette (GEN2) is attached to.\n* Number of Samples: Specify the number of samples to be run. Currently, 8 is the only number allowed.\n", "internal": "gna_octea", "labware": "\nOpentrons 200\u00b5L Filter Tips\nNEST 96-Deep Well Plate, 2mL\nBio-Rad 96-Well Plate\nNEST 12-Well Reservoir, 15mL\nCustom Plate for GNA Octea Chip\n", "markdown": { @@ -33,7 +33,7 @@ "pipettes": "\nP300 Multi-Channel Pipette (GEN2)\nP300 Single-Channel Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions), if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\nThe Temperature Module (GEN2) will heat to 90\u00b0C and the Magnetic Module (GEN2) will engage.\nThe P300 Single-Channel Pipette (GEN2) will pick up a tip, transfer 360\u00b5L of HB1 to MB Lyo, mix and distribute 40\u00b5L of mixture to wells adjacent to wells containing samples in NEST 96-Deep Well Plate, 2mL.\nThe P300 Multi-Channel Pipette (GEN2) will transfer HB1 to NEST 96-Deep Well Plate, 2mL - 360\u00b5L to previous wells and 300\u00b5L to wells containing samples, changing tips between these steps.\nUsing the same tips from the previous step, the P300 Multi-Channel Pipette (GEN2) will transfer the sample+HB1 mixture to the adjacent wells, mix, and trash the tips.\nUsing a new set of tips, the P300 Multi-Channel Pipette (GEN2) will transfer 160\u00b5L to the first 5 columns of the Bio-Rad 96-Well Plate sitting on the 96-Well Aluminum Block on top of the Temperature Module (GEN2).\nThe Temperature Module (GEN2) will change its temperature from 90\u00b0C to 80\u00b0C. Once the desired temperature is reached, the protocol will delay for two minutes. At the conclusion of this delay/incubation, the Temperature Module (GEN2) will change its temperature to 56\u00b0C. The P300 Multi-Channel Pipette (GEN2) will mix all of the samples on the Temperature Module (GEN2) and after mixing, the Temperature Module (GEN2) will deactivate.\nUsing the tips from the previous steps, the P300 Multi-Channel Pipette (GEN2) will transfer the samples from the Temperature Module (GEN2) to the corresponding wells of the Bio-Rad plate on the Magnetic Module (GEN2). The protocol will then delay for three minutes.\nThe P300 Multi-Channel Pipette (GEN2) will pick up a new set of tips and lower the flow rate to remove the supernatant and discard in the liquid waste (Well 12 of the NEST 12-Well Reservoir).\nThe P300 Multi-Channel Pipette (GEN2) will pick up a new set of tips and will transfer WB1 to samples on the Magnetic Module (GEN2), mix, and recombine the samples in column 5.\nThe Magnetic Module (GEN2) will engage and the protocol will delay for three minutes. After the delay, the P300 Multi-Channel Pipette (GEN2) will remove supernatant from the sample wells and discard in the liquid waste.\nThe P300 Single-Channel Pipette (GEN2) will transfer 350\u00b5L RB1 to the well containing the MM Lyo, mix, and distribute 40\u00b5L to the sample wells on the Magnetic Module (GEN2).\nThe P300 Multi-Channel Pipette (GEN2) will pick up a new set of tips and mix the samples in column 5 on the Magnetic Module (GEN2) containing sample and RB1+MM Lyo.\nFor each well containing sample on the Magnetic Module (GEN2) (8), the P300 Single-Channel Pipette (GEN2) will pick up a new tip and transfer to the corresponding well on the custom plate containing the GNA Octea Chip.\n", - "reagent-setup": "NEST 12-Well Reservoir, 15mL (Deck Slot 7)\n* Well 1: WB1\n* Well 3: HB1\n* Well 12: Liquid Waste (Empty)\nNEST 96-Deep Well Plate, 2mL (Deck Slot 8)\n* Column 1/A1-H1: Samples\n* A12: RB1\n* D11: MB Lyo\n* D12: MM Lyo\n", + "reagent-setup": "NEST 12-Well Reservoir, 15mL (Deck Slot 7)\n Well 1: WB1\n Well 3: HB1\n* Well 12: Liquid Waste (Empty)\nNEST 96-Deep Well Plate, 2mL (Deck Slot 8)\n Column 1/A1-H1: Samples\n A12: RB1\n D11: MB Lyo\n D12: MM Lyo\n", "reagents": [ "WB1", "RB1", diff --git a/protoBuilds/gna_octea_v2/README.json b/protoBuilds/gna_octea_v2/README.json index 7eac969be..b77c05611 100644 --- a/protoBuilds/gna_octea_v2/README.json +++ b/protoBuilds/gna_octea_v2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol automates GNA Octea prep. Using the P300 Multi-Channel Pipette (GEN2) and the P300 Single-Channel Pipette (GEN2), all the reagents necessary for the sample prep are transferred to the samples and the samples are incubated on the Temperature Module and Magnetic Module. Once all sample prep has been completed, the samples are transferred to a custom plate containing the labware needed to test the samples on the GNA analyzer.\nThis protocol is still a work in progress and will be updated.\nExplanation of complex parameters below:\n* P300-Multi Mount: Select which mount the P300 Multi-Channel Pipette (GEN2) is attached to.\n* P300-Single Mount: Select which mount the P300 Single-Channel Pipette (GEN2) is attached to.\n* Labware on Temp Deck + Al Block: Select which tube type will contain the samples.\n* Reconstitue MagBeads/PCA?: Specify whether the OT-2 will reconstitute the MagBeads and PCA.\n", + "description": "This protocol automates GNA Octea prep. Using the P300 Multi-Channel Pipette (GEN2) and the P300 Single-Channel Pipette (GEN2), all the reagents necessary for the sample prep are transferred to the samples and the samples are incubated on the Temperature Module and Magnetic Module. Once all sample prep has been completed, the samples are transferred to a custom plate containing the labware needed to test the samples on the GNA analyzer.\nThis protocol is still a work in progress and will be updated.\nExplanation of complex parameters below:\n P300-Multi Mount: Select which mount the P300 Multi-Channel Pipette (GEN2) is attached to.\n P300-Single Mount: Select which mount the P300 Single-Channel Pipette (GEN2) is attached to.\n Labware on Temp Deck + Al Block: Select which tube type will contain the samples.\n Reconstitue MagBeads/PCA?: Specify whether the OT-2 will reconstitute the MagBeads and PCA.\n", "internal": "gna_octea_v2", "labware": "\nOpentrons 200\u00b5L Filter Tips\nNEST 96-Deep Well Plate, 2mL\nNEST 12-Well Reservoir, 15mL\nOpentrons Tube Rack\n1.5mL (and/or 2mL) Microcentrigue Tubes\nCustom Plate for GNA Octea Chip\n", "markdown": { @@ -33,7 +33,7 @@ "pipettes": "\nP300 Multi-Channel Pipette (GEN2)\nP300 Single-Channel Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions), if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\nThe protocol begins with the Single-Channel Pipette transferring 10\u00b5L of Magnetic Beads to the 8 samples. The Magnetic Beads are mixed before aspiration and RS1 is added if selected above. The same tip is used for all transfers.\nThe Single-Channel Pipette picks up a tip, transfers 680\u00b5L HB1 (170\u00b5L, 4x) to the sample, mixes 10 times, performs a touch tip, then drops tip in waste (for each sample).\nThe Temperature Module is set to 80C and the protocol delays for 3 minutes (incubation).\nThe Temperature Module is set to 56C. While the Temperature Module is cooling, the Single-Channel Pipette will mix the samples.\nAfter a 3 minute incubation at 56C, the Single-Channel Pipette will transfer samples to the Deepwell Plate on the Magnetic Module\nThe Magnetic Module will engage and the protocol will delay for 2 minutes (incubation). After the delay, the Multi-Channel Pipette will transfer the supernatant (160\u00b5L, 5x) to A1 of the 12-Well Reservoir.\nThe Multi-Channel Pipette, using new tips, will transfer 200\u00b5l of WB1 and mix 12 times.\nAgain, the Magnetic Module will engage and the protocol will delay for 2 minutes (incubation). After the delay, the Multi-Channel Pipette will transfer the supernatant (200\u00b5L) to A1 of the 12-Well Reservoir.\nThe Single-Channel Pipette, using a single tip, will transfer 40\u00b5L of PCA to each of the sample wells in the Deepwell Plate, reconstituting the PCA beforehand if selected.\nUsing a new tip for each sample, the Single-Channel Pipette will mix the sample and transfer 40\u00b5L to the GNA Octea well.\n", - "reagent-setup": "NEST 12-Well Reservoir, 15mL (Deck Slot 10)\n* Well 12: HB1\n* Well 10: HB1\n* Well 1: Liquid Waste (Empty)\n\n\nOpentrons Tube Rack (Deck Slot 6)\n* A1: Magnetic Beads\n* A6: PCA\n* D6: RS1, is using\n\n", + "reagent-setup": "NEST 12-Well Reservoir, 15mL (Deck Slot 10)\n Well 12: HB1\n Well 10: HB1\n Well 1: Liquid Waste (Empty)\n\n\nOpentrons Tube Rack (Deck Slot 6)\n A1: Magnetic Beads\n A6: PCA\n D6: RS1, is using\n\n", "reagents": [ "WB1", "RS1", diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json b/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json index 5797f97a8..3396fcdc8 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json @@ -5,7 +5,7 @@ "NGS Library Prep: Illumina Nextera XT" ] }, - "description": "Part 1 of 4: Tagment Genomic DNA and Amplify Libraries\nLinks:\n* Part 1: Tagment and Amplify\n* Part 2: Clean Up Libraries\n* Part 3: Normalize Libraries\n* Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol described by the Illumina Reference Guide.\nThis is part 1 of the protocol, which includes the steps (1) Tagment Genomic DNA and (2) Amplify Libraries.\nThe tagmentation step uses Nextera transposase to fragment DNA into sizes suitable for sequencing, and then tags the DNA with adapter sequences. The library amplification step increases the yield of the tagmented DNA using PCR. PCR adds the Index 1 (i7), Index 2 (i5), and full adapter sequences to the tagmented DNA from the previous step. This protocol assumes you are taking your plate off the OT-2 and thermocycling on a stand-alone PCR machine according to the Illumina Reference Guide.\nAfter the two steps carried out in this protocol, you can safely stop work and return to it at a later point. If you are stopping, seal the plate and store at 2\u00b0C to 8\u00b0C for up to 2 days.", + "description": "Part 1 of 4: Tagment Genomic DNA and Amplify Libraries\nLinks:\n Part 1: Tagment and Amplify\n Part 2: Clean Up Libraries\n Part 3: Normalize Libraries\n Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol described by the Illumina Reference Guide.\nThis is part 1 of the protocol, which includes the steps (1) Tagment Genomic DNA and (2) Amplify Libraries.\nThe tagmentation step uses Nextera transposase to fragment DNA into sizes suitable for sequencing, and then tags the DNA with adapter sequences. The library amplification step increases the yield of the tagmented DNA using PCR. PCR adds the Index 1 (i7), Index 2 (i5), and full adapter sequences to the tagmented DNA from the previous step. This protocol assumes you are taking your plate off the OT-2 and thermocycling on a stand-alone PCR machine according to the Illumina Reference Guide.\nAfter the two steps carried out in this protocol, you can safely stop work and return to it at a later point. If you are stopping, seal the plate and store at 2\u00b0C to 8\u00b0C for up to 2 days.", "internal": "bU7eUGEh\n872", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json b/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json index 1a9fba304..56b336260 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json @@ -5,7 +5,7 @@ "NGS Library Prep: Illumina Nextera XT" ] }, - "description": "Part 2 of 4: Clean Up Libraries\nLinks:\n* Part 1: Tagment and Amplify\n* Part 2: Clean Up Libraries\n* Part 3: Normalize Libraries\n* Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol describe by the Illumina Reference Guide.\nThis is Part 2 of the protocol, which consists of just step (3) of the overall process: clean up libraries. This step uses AMPure XP beads to purify the library DNA and remove short library fragments after the previous step, library amplification.\nAfter this step, it is safe to stop the workflow and return to it at a later point. If you are stopping, seal the plate and store at -15\u00b0C to -25\u00b0C for up to seven days.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P300 or P50 Pipette (Single or 8-Channel) and corresponding Tips\nOpentrons Magnetic Module\nBio-Rad 96-Well Plate, 200\u03bcl containing samples from Part 1\nBio-Rad 96-Well Plate, 200\u03bcl, clean and empty (x2)\nUSA Scientific 12-Channel Reservoir\nNextera XT DNA Library Prep Kit\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThis protocol requires specific labware in a specific set-up.\nSlot 1: Bio-Rad Plate (clean and empty); final elution will be transferred to this plate.\nSlot 2: USA Scientific 12-Channel Reservoir\n* A1: Resuspension Buffer\n* A2: AMPure XP Beads\n* A3: 80% Ethanol\n* A4: 80% Ethanol (if needed)\n* A5: 80% Ethanol (if needed)\n* A9: Liquid Waste\n* A10: Liquid Waste\n* A11: Liquid Waste\n* A12: Liquid Waste\nSlot 4: Magnetic Module with Bio-Rad Plate (clean and empty)\nSlot 5: Bio-Rad Plate containing samples from Part 1\nSlot 6: Opentrons Tip Rack\nSlot 7: Opentrons Tip Rack\nSlot 8: Opentrons Tip Rack\n* Note: If your protocol requires more tips due to the parameters you set, you will need to fill subsequent slots with tip racks.\nUsing the customization fields below, set up your protocol.\n* Pipette Model: Select which pipette (P50/P300; Single/8-Channel) you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n* Magnetic Module Gen: Specify which Magnetic Module is in use\n* Number of Samples: Select the number of samples (1-96) to be run in the protocol.\n* Initial Product Volume (\u00b5l): Select the starting volume of PCR product to be used in the protocol.\n* Bead Ratio: Select the bead ratio. 1.8 is recommended for small (300-500 bp) inputs, and 0.6 is recommended for larger (>500 bp) samples. Please see documentation for more information.\n* Resuspension Buffer Volume (\u00b5L): Specify how much Resuspension Buffer is added to the wells.\n* Final PCR Product Volume (\u00b5L): Specify the final elution volume to be transferred.\n* Dry Time (minutes): Specify how long (in minutes) you would like to let the beads dry after the wash steps and before adding the resuspension buffer.", + "description": "Part 2 of 4: Clean Up Libraries\nLinks:\n Part 1: Tagment and Amplify\n Part 2: Clean Up Libraries\n Part 3: Normalize Libraries\n Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol describe by the Illumina Reference Guide.\nThis is Part 2 of the protocol, which consists of just step (3) of the overall process: clean up libraries. This step uses AMPure XP beads to purify the library DNA and remove short library fragments after the previous step, library amplification.\nAfter this step, it is safe to stop the workflow and return to it at a later point. If you are stopping, seal the plate and store at -15\u00b0C to -25\u00b0C for up to seven days.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P300 or P50 Pipette (Single or 8-Channel) and corresponding Tips\nOpentrons Magnetic Module\nBio-Rad 96-Well Plate, 200\u03bcl containing samples from Part 1\nBio-Rad 96-Well Plate, 200\u03bcl, clean and empty (x2)\nUSA Scientific 12-Channel Reservoir\nNextera XT DNA Library Prep Kit\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThis protocol requires specific labware in a specific set-up.\nSlot 1: Bio-Rad Plate (clean and empty); final elution will be transferred to this plate.\nSlot 2: USA Scientific 12-Channel Reservoir\n A1: Resuspension Buffer\n A2: AMPure XP Beads\n A3: 80% Ethanol\n A4: 80% Ethanol (if needed)\n A5: 80% Ethanol (if needed)\n A9: Liquid Waste\n A10: Liquid Waste\n A11: Liquid Waste\n* A12: Liquid Waste\nSlot 4: Magnetic Module with Bio-Rad Plate (clean and empty)\nSlot 5: Bio-Rad Plate containing samples from Part 1\nSlot 6: Opentrons Tip Rack\nSlot 7: Opentrons Tip Rack\nSlot 8: Opentrons Tip Rack\n* Note: If your protocol requires more tips due to the parameters you set, you will need to fill subsequent slots with tip racks.\nUsing the customization fields below, set up your protocol.\n Pipette Model: Select which pipette (P50/P300; Single/8-Channel) you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n Magnetic Module Gen: Specify which Magnetic Module is in use\n Number of Samples: Select the number of samples (1-96) to be run in the protocol.\n Initial Product Volume (\u00b5l): Select the starting volume of PCR product to be used in the protocol.\n Bead Ratio: Select the bead ratio. 1.8 is recommended for small (300-500 bp) inputs, and 0.6 is recommended for larger (>500 bp) samples. Please see documentation for more information.\n Resuspension Buffer Volume (\u00b5L): Specify how much Resuspension Buffer is added to the wells.\n Final PCR Product Volume (\u00b5L): Specify the final elution volume to be transferred.\n* Dry Time (minutes): Specify how long (in minutes) you would like to let the beads dry after the wash steps and before adding the resuspension buffer.", "internal": "bU7eUGEh\n872", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part3/README.json b/protoBuilds/illumina-nextera-XT-library-prep-part3/README.json index 409eda0d4..7cfa293d1 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part3/README.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part3/README.json @@ -5,7 +5,7 @@ "NGS Library Prep: Illumina Nextera XT" ] }, - "description": "Part 3 of 4: Normalize Libraries\nLinks:\n* Part 1: Tagment and Amplify\n* Part 2: Clean Up Libraries\n* Part 3: Normalize Libraries\n* Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol describe by the Illumina Reference Guide.\nThis is part 3 of the protocol, which is step (4) of the overall workflow: normalize libraries. This step normalizes the concentration of each library to ensure correct library representation in the donwstream pooled libraries.\nIt is safe to stop after this step and re-start work at a later point. If you are stopping, seal the plate and store at -25\u00b0C to -15\u00b0C for up to seven days.\n--\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P300 or P50 Pipette (Single or 8-Channel) and corresponding Tips\nOpentrons Magnetic Module\nBio-Rad 96-Well Plate, 200\u03bcl containing samples from Part 1\nBio-Rad 96-Well Plate, 200\u03bcl, clean and empty (x2)\nUSA Scientific 12-Channel Reservoir\nNextera XT DNA Library Prep Kit\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThis protocol requires specific labware in a specific set-up.\nSlot 1: Bio-Rad Plate (clean and empty); final elution will be transferred to this plate.\nSlot 2: USA Scientific 12-Channel Reservoir\n* A1: Library Normalization Additive 1 (LNA1)\n* A2: Library Normalization Beads 1 (LNB1)\n* A3: Library Normalization Wash 1 (LNW1)\n* A4: Library Normalization Storage Buffer 1 (LNS1)\n* A5: 0.1 N NaOH\n* A6: Empty - LNA1 & LNB1 will be combined here, if not pre-mixed\n* A12: Liquid Waste\nSlot 4: Magnetic Module with Bio-Rad Plate (clean and empty)\nSlot 5: Bio-Rad Plate containing samples from Part 2\nSlot 7: Opentrons Tip Rack\nSlot 8: Opentrons Tip Rack\nSlot 9: Opentrons Tip Rack\nUsing the customization fields below, set up your protocol.\n* Pipette Model: Select which pipette (P50/P300) you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n* Number of Samples: Select the number of samples (1-96) to be run in the protocol. NOTE ~ selecting 24 or less samples will result in only the top-left corner of the plates being used (A1 - D6).\n* Mix LNA1 & LNB1 with OT-2: Select whether the OT-2 should mix the LNA1 or LNB1 together. If yes, the OT-2 will transfer the reagents from A1 and A2 of the reservoir, respectively, and mix in A6. Otherwise, the pre-mixed reagent should be loaded directly in A6 of the 12-well reservoir.", + "description": "Part 3 of 4: Normalize Libraries\nLinks:\n Part 1: Tagment and Amplify\n Part 2: Clean Up Libraries\n Part 3: Normalize Libraries\n Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol describe by the Illumina Reference Guide.\nThis is part 3 of the protocol, which is step (4) of the overall workflow: normalize libraries. This step normalizes the concentration of each library to ensure correct library representation in the donwstream pooled libraries.\nIt is safe to stop after this step and re-start work at a later point. If you are stopping, seal the plate and store at -25\u00b0C to -15\u00b0C for up to seven days.\n--\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons P300 or P50 Pipette (Single or 8-Channel) and corresponding Tips\nOpentrons Magnetic Module\nBio-Rad 96-Well Plate, 200\u03bcl containing samples from Part 1\nBio-Rad 96-Well Plate, 200\u03bcl, clean and empty (x2)\nUSA Scientific 12-Channel Reservoir\nNextera XT DNA Library Prep Kit\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThis protocol requires specific labware in a specific set-up.\nSlot 1: Bio-Rad Plate (clean and empty); final elution will be transferred to this plate.\nSlot 2: USA Scientific 12-Channel Reservoir\n A1: Library Normalization Additive 1 (LNA1)\n A2: Library Normalization Beads 1 (LNB1)\n A3: Library Normalization Wash 1 (LNW1)\n A4: Library Normalization Storage Buffer 1 (LNS1)\n A5: 0.1 N NaOH\n A6: Empty - LNA1 & LNB1 will be combined here, if not pre-mixed\n* A12: Liquid Waste\nSlot 4: Magnetic Module with Bio-Rad Plate (clean and empty)\nSlot 5: Bio-Rad Plate containing samples from Part 2\nSlot 7: Opentrons Tip Rack\nSlot 8: Opentrons Tip Rack\nSlot 9: Opentrons Tip Rack\nUsing the customization fields below, set up your protocol.\n Pipette Model: Select which pipette (P50/P300) you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n Number of Samples: Select the number of samples (1-96) to be run in the protocol. NOTE ~ selecting 24 or less samples will result in only the top-left corner of the plates being used (A1 - D6).\n Mix LNA1 & LNB1 with OT-2: Select whether the OT-2 should mix the LNA1 or LNB1 together. If yes, the OT-2 will transfer the reagents from A1 and A2 of the reservoir, respectively, and mix in A6. Otherwise, the pre-mixed reagent should be loaded directly in A6 of the 12-well reservoir.", "internal": "bU7eUGEh\n872", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part4/README.json b/protoBuilds/illumina-nextera-XT-library-prep-part4/README.json index 0168c560d..415e83edc 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part4/README.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part4/README.json @@ -5,7 +5,7 @@ "NGS Library Prep: Illumina Nextera XT" ] }, - "description": "Part 4 of 4: Pool Libraries\nLinks:\n* Part 1: Tagment and Amplify\n* Part 2: Clean Up Libraries\n* Part 3: Normalize Libraries\n* Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol described by the Illumina Reference Guide.\nThis is part 4 of the protocol, which is step (4) pool libraries. This step combines equal volumes of normalized libraries in a single tube. After pooling, dilute and heat-denature the library pool before loading libraries for the sequencing run.\nStore unused pooled libraries in the PAL tube and SGP plate at -25\u00b0C to -15\u00b0C for up to 7 days.\n--\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nBio-Rad 96-Well Plate, 200\u03bcl containing samples from Part 3\nOpentrons Tube Rack with 2mL tubes\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThis protocol requires specific labware in a specific set-up.\nSlot 1: Bio-Rad Plate containing samples from Part 3\nSlot 2: Tube Rack with 2mL tubes (for collecting pools)\nSlot 3: Opentrons Tip Rack\n* Note: If your protocol requires more tips due to the parameters you set, you will need to fill subsequent slots with tip racks.\nUsing the customization fields below, set up your protocol.\n* Pipette Model: Select which pipette you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n* Number of Samples: Select the number of samples (1-96) to be run in the protocol. NOTE ~ selecting 24 or less samples will result in only the top-left corner of the plates being used (A1 - D6).\n* Number of Pools: Select the number of pools (2mL tubes) that should be created from the sample plate.\n* Pool Volume (\u03bcl): Select the amount (in microliters) of sample material to transfer to each pooling tube.", + "description": "Part 4 of 4: Pool Libraries\nLinks:\n Part 1: Tagment and Amplify\n Part 2: Clean Up Libraries\n Part 3: Normalize Libraries\n Part 4: Pool Libraries\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol described by the Illumina Reference Guide.\nThis is part 4 of the protocol, which is step (4) pool libraries. This step combines equal volumes of normalized libraries in a single tube. After pooling, dilute and heat-denature the library pool before loading libraries for the sequencing run.\nStore unused pooled libraries in the PAL tube and SGP plate at -25\u00b0C to -15\u00b0C for up to 7 days.\n--\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nBio-Rad 96-Well Plate, 200\u03bcl containing samples from Part 3\nOpentrons Tube Rack with 2mL tubes\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThis protocol requires specific labware in a specific set-up.\nSlot 1: Bio-Rad Plate containing samples from Part 3\nSlot 2: Tube Rack with 2mL tubes (for collecting pools)\nSlot 3: Opentrons Tip Rack\n* Note: If your protocol requires more tips due to the parameters you set, you will need to fill subsequent slots with tip racks.\nUsing the customization fields below, set up your protocol.\n Pipette Model: Select which pipette you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right).\n Number of Samples: Select the number of samples (1-96) to be run in the protocol. NOTE ~ selecting 24 or less samples will result in only the top-left corner of the plates being used (A1 - D6).\n Number of Pools: Select the number of pools (2mL tubes) that should be created from the sample plate.\n* Pool Volume (\u03bcl): Select the amount (in microliters) of sample material to transfer to each pooling tube.", "internal": "bU7eUGEh\n872", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/magnesil/README.json b/protoBuilds/magnesil/README.json index cef9bb841..22c0387dd 100644 --- a/protoBuilds/magnesil/README.json +++ b/protoBuilds/magnesil/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\n\nSlot 2: 12-Well Reservoir (See Reagent Setup below for more information)\n\nSlot 4: Opentrons Magnetic Module with 96-Deepwell Plate containing samples in odd columns (during the protocol, samples will be transferred to the even columns)\n\n\nSlot 6: 96-Well Plate for elutes\n\nSlots 7-11: Opentrons Tips (Each column of samples requires 15 columns of tips)", - "description": "This protocol performs a nucleic acid purification protocol based on the MagneSil Plasmid Purification System from Promega. Using flexible parameters (described below), one can adapt this protocol to the equipment in their lab and modify to their workflow.\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples (1-32)\n* Pipette Model: Select between the GEN1 and GEN2 P300 8-Channel Pipette\n* Pipette Mount: Select which mount (Right, Left) the pipette is attached to\n* Use Filter Tips?: Select whether to use Opentrons 200\u00b5L Filter Tips or Opentrons 300\u00b5L Standard Tips\n* Magnetic Module Model: Select between the GEN1 and GEN2 Opentrons Magnetic Module\n* Sample Plate Type: Select the type of plate containing samples (will be placed on Magnetic Module)\n* Reservoir Type: Select which 12-Well Reservoir will be used to hold reagents\n* Elution Plate Type: Select the type of plate that will be used for the elutions\n", + "description": "This protocol performs a nucleic acid purification protocol based on the MagneSil Plasmid Purification System from Promega. Using flexible parameters (described below), one can adapt this protocol to the equipment in their lab and modify to their workflow.\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples (1-32)\n Pipette Model: Select between the GEN1 and GEN2 P300 8-Channel Pipette\n Pipette Mount: Select which mount (Right, Left) the pipette is attached to\n Use Filter Tips?: Select whether to use Opentrons 200\u00b5L Filter Tips or Opentrons 300\u00b5L Standard Tips\n Magnetic Module Model: Select between the GEN1 and GEN2 Opentrons Magnetic Module\n Sample Plate Type: Select the type of plate containing samples (will be placed on Magnetic Module)\n Reservoir Type: Select which 12-Well Reservoir will be used to hold reagents\n Elution Plate Type: Select the type of plate that will be used for the elutions\n", "internal": "magnesil", "labware": "\nOpentrons Tips for P300 (Filter or Standard)\n96-Deepwell Plate (containing samples) (Example)\n12-Well Reservoir (Example)\n96-Well Plate (Example)\n", "markdown": { diff --git a/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/README.json b/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/README.json index e1dae0fca..5b1d9e74f 100644 --- a/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/README.json +++ b/protoBuilds/nextera-flex-library-prep-amplify-tagmented-dna/README.json @@ -5,7 +5,7 @@ "Nextera DNA Flex Library Prep" ] }, - "description": "This protocol performs the 'Amplify Tagmented DNA' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n* Cherrypick Samples\n* Tagment DNA\n* Post Tagmentation Cleanup\n* Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOpentrons magnetic module\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nAgilent single-channel reservoir 290ml #201252-100\nOpentrons 4-in-1 tuberack with 2ml Eppendorf tubes\nP50 Single-channel electronic pipette\nP300 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nPreprogram the thermocycler according to the BLT PCR program parameters described in the kit manual.\n4x6 aluminum block tuberack (slot 4, mounted on temperature module)\n* A1-C1: mastermix 1.5ml snapcap tubes (loaded empty, 1 tube needed per 32 samples)\n* A2-D2: EPM in 0.5ml false-bottom tubes (1 tube needed per 24 samples)\n* A3-B3: nuclease-free water in 1.5ml snapcap tubes (1 tube needed per 48 samples)", + "description": "This protocol performs the 'Amplify Tagmented DNA' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n Cherrypick Samples\n Tagment DNA\n Post Tagmentation Cleanup\n Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOpentrons magnetic module\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nAgilent single-channel reservoir 290ml #201252-100\nOpentrons 4-in-1 tuberack with 2ml Eppendorf tubes\nP50 Single-channel electronic pipette\nP300 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nPreprogram the thermocycler according to the BLT PCR program parameters described in the kit manual.\n4x6 aluminum block tuberack (slot 4, mounted on temperature module)\n A1-C1: mastermix 1.5ml snapcap tubes (loaded empty, 1 tube needed per 32 samples)\n A2-D2: EPM in 0.5ml false-bottom tubes (1 tube needed per 24 samples)\n* A3-B3: nuclease-free water in 1.5ml snapcap tubes (1 tube needed per 48 samples)", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", "categories": "* NGS Library Prep\n\t* Nextera DNA Flex Library Prep\n\n\n", diff --git a/protoBuilds/nextera-flex-library-prep-cherrypick-samples/README.json b/protoBuilds/nextera-flex-library-prep-cherrypick-samples/README.json index f6c62f680..5b3f67b39 100644 --- a/protoBuilds/nextera-flex-library-prep-cherrypick-samples/README.json +++ b/protoBuilds/nextera-flex-library-prep-cherrypick-samples/README.json @@ -5,7 +5,7 @@ "Nextera DNA Flex Library Prep" ] }, - "description": "This protocol cherrypicks samples from up to 9 Olympus PCR source plates to 1 Bio-Rad Hard Shell PCR destination plate as preparation for the the Nextera DNA Flex Library Prep protocol. The CSV should be formatted in the following format, including the header line:\nSource plate (1-9), Source well (A1-H12), Destination well (A1-H12)\n1, A1, A1\n1, C5, A2\n3, H9, A3\n9, E3, B1\nLinks:\n* Cherrypick Samples\n* Tagment DNA\n* Post Tagmentation Cleanup\n* Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOlympus 96-well PCR plates 200ul\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nP50/P300 Single-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nPreprogram the thermocycler according to the BLT PCR program parameters described in the kit manual.\n4x6 aluminum block tuberack (slot 4, mounted on temperature module)\n* A1-C1: mastermix 1.5ml snapcap tubes (loaded empty, 1 tube needed per 32 samples)\n* A2-D2: EPM in 0.5ml false-bottom tubes (1 tube needed per 24 samples)\n* A3-B3: nuclease-free water in 1.5ml snapcap tubes (1 tube needed per 48 samples)", + "description": "This protocol cherrypicks samples from up to 9 Olympus PCR source plates to 1 Bio-Rad Hard Shell PCR destination plate as preparation for the the Nextera DNA Flex Library Prep protocol. The CSV should be formatted in the following format, including the header line:\nSource plate (1-9), Source well (A1-H12), Destination well (A1-H12)\n1, A1, A1\n1, C5, A2\n3, H9, A3\n9, E3, B1\nLinks:\n Cherrypick Samples\n Tagment DNA\n Post Tagmentation Cleanup\n Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOlympus 96-well PCR plates 200ul\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nP50/P300 Single-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nPreprogram the thermocycler according to the BLT PCR program parameters described in the kit manual.\n4x6 aluminum block tuberack (slot 4, mounted on temperature module)\n A1-C1: mastermix 1.5ml snapcap tubes (loaded empty, 1 tube needed per 32 samples)\n A2-D2: EPM in 0.5ml false-bottom tubes (1 tube needed per 24 samples)\n* A3-B3: nuclease-free water in 1.5ml snapcap tubes (1 tube needed per 48 samples)", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", "categories": "* NGS Library Prep\n\t* Nextera DNA Flex Library Prep\n\n\n", diff --git a/protoBuilds/nextera-flex-library-prep-cleanup-libraries/README.json b/protoBuilds/nextera-flex-library-prep-cleanup-libraries/README.json index ef6199f5d..ed12a1191 100644 --- a/protoBuilds/nextera-flex-library-prep-cleanup-libraries/README.json +++ b/protoBuilds/nextera-flex-library-prep-cleanup-libraries/README.json @@ -5,7 +5,7 @@ "Nextera DNA Flex Library Prep" ] }, - "description": "This protocol performs the 'Cleanup Libraries' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n* Cherrypick Samples\n* Tagment DNA\n* Post Tagmentation Cleanup\n* Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOpentrons magnetic module\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nOpentrons 4-in-1 tuberack with 2ml Eppendorf tubes\nP50 Single/multi-channel electronic pipette\nP300 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nCentrifuge the PCR plate from the Amplify Tagmented DNA step. Place the plate on the magnetic module.\n12-channel reservoir (slot 3)\n* channel 1: SPB (user is prompted to vortex before adding mid-protocol)\n* channel 2: nuclease-free water\n* channel 3: RSB\n* channel 4-5: EtOH\n* channels 10-12: liquid waste (loaded empty)", + "description": "This protocol performs the 'Cleanup Libraries' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n Cherrypick Samples\n Tagment DNA\n Post Tagmentation Cleanup\n Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOpentrons magnetic module\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nOpentrons 4-in-1 tuberack with 2ml Eppendorf tubes\nP50 Single/multi-channel electronic pipette\nP300 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nCentrifuge the PCR plate from the Amplify Tagmented DNA step. Place the plate on the magnetic module.\n12-channel reservoir (slot 3)\n channel 1: SPB (user is prompted to vortex before adding mid-protocol)\n channel 2: nuclease-free water\n channel 3: RSB\n channel 4-5: EtOH\n* channels 10-12: liquid waste (loaded empty)", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", "categories": "* NGS Library Prep\n\t* Nextera DNA Flex Library Prep\n\n", diff --git a/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/README.json b/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/README.json index 95b5b18c9..db69ab2d7 100644 --- a/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/README.json +++ b/protoBuilds/nextera-flex-library-prep-post-tag-cleanup/README.json @@ -5,7 +5,7 @@ "Nextera DNA Flex Library Prep" ] }, - "description": "This protocol performs the 'Post Tagmentation Cleanup' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n* Cherrypick Samples\n* Tagment DNA\n* Post Tagmentation Cleanup\n* Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOpentrons magnetic module\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nP300 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nAdd 10ul of TSB to each sample, seal the plate with Microseal B, place on the preprogrammed thermal cycler, and run the PTC program.\n12-channel reservoir (slot 3)\n* channel 1: TWB\n* channel 2: TWB (only needed if number of samples > 48)\n* channel 12: liquid waste (loaded empty)", + "description": "This protocol performs the 'Post Tagmentation Cleanup' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n Cherrypick Samples\n Tagment DNA\n Post Tagmentation Cleanup\n Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nOpentrons magnetic module\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nUSA Scientific 12-channel reservoir 22ml #1061-8150\nP300 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nAdd 10ul of TSB to each sample, seal the plate with Microseal B, place on the preprogrammed thermal cycler, and run the PTC program.\n12-channel reservoir (slot 3)\n channel 1: TWB\n channel 2: TWB (only needed if number of samples > 48)\n* channel 12: liquid waste (loaded empty)", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", "categories": "* NGS Library Prep\n\t* Nextera DNA Flex Library Prep\n\n\n", diff --git a/protoBuilds/nextera-flex-library-prep-tagment-dna/README.json b/protoBuilds/nextera-flex-library-prep-tagment-dna/README.json index 810b0cee4..627c44aac 100644 --- a/protoBuilds/nextera-flex-library-prep-tagment-dna/README.json +++ b/protoBuilds/nextera-flex-library-prep-tagment-dna/README.json @@ -5,7 +5,7 @@ "Nextera DNA Flex Library Prep" ] }, - "description": "This protocol performs the 'Tagment DNA' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n* Cherrypick Samples\n* Tagment DNA\n* Post Tagmentation Cleanup\n* Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nOpentrons 4-in-1 tuberack with 1.5ml Eppendorf tubes\n200ul PCR strips\nP50 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nVortex BLT and TB1 vigorously for 10 seconds before placing in tube rack wells B1 and C1, respectively, and resuming. Preprogram the thermocycler according to the TAG program parameters described in the kit manual.\n1.5ml Eppendorf Tuberack (slot 2)\n* A1-B1: mastermix 1.5ml snapcap tubes (loaded empty, 1 tube needed per 48 samples)\n* A2-B2: BLT in 0.5ml false-bottom tubes (1 tube needed per 48 samples)\n* A3-B3: TB1 in 0.5ml false-bottom tubes (1 tube needed per 48 samples)\n200ul PCR strips (slot 3 only needed if using P50 multi-channel pipette\n* strip column 1: mastermix strip (loaded empty)", + "description": "This protocol performs the 'Tagment DNA' section of the Nextera DNA Flex Library Prep protocol.\nLinks:\n Cherrypick Samples\n Tagment DNA\n Post Tagmentation Cleanup\n Amplify Tagmented DNA\n* Cleanup Libraries\n\n\n\nBio-Rad Hard Shell 96-well low profile PCR plate 200ul #hsp9601\nOpentrons 4-in-1 tuberack with 1.5ml Eppendorf tubes\n200ul PCR strips\nP50 Single/multi-channel electronic pipette\n300ul Opentrons tipracks\n\n\n\nVortex BLT and TB1 vigorously for 10 seconds before placing in tube rack wells B1 and C1, respectively, and resuming. Preprogram the thermocycler according to the TAG program parameters described in the kit manual.\n1.5ml Eppendorf Tuberack (slot 2)\n A1-B1: mastermix 1.5ml snapcap tubes (loaded empty, 1 tube needed per 48 samples)\n A2-B2: BLT in 0.5ml false-bottom tubes (1 tube needed per 48 samples)\n* A3-B3: TB1 in 0.5ml false-bottom tubes (1 tube needed per 48 samples)\n200ul PCR strips (slot 3 only needed if using P50 multi-channel pipette\n* strip column 1: mastermix strip (loaded empty)", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", "categories": "* NGS Library Prep\n\t* Nextera DNA Flex Library Prep\n\n\n", diff --git a/protoBuilds/normalization/README.json b/protoBuilds/normalization/README.json index 27b4b300e..2d5c20e6d 100644 --- a/protoBuilds/normalization/README.json +++ b/protoBuilds/normalization/README.json @@ -5,7 +5,7 @@ "Normalization" ] }, - "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library prep. With this protocol, you can easily normalize the concentrations of samples in a 96 or 384 microwell plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nSamples in a compatible plate (96-well or 384-well)\nAutomation-friendly reservoir\nDiluent\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nCSV Format\nYour file must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). It should be formatted in \u201clandscape\u201d orientation, with the value corresponding to well A1 in the upper left-hand corner of the value list.\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, and so on.\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV from there.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).\nUsing the customization fields below, set up your protocol.\n* Volumes CSV: Upload the CSV (.csv) containing your diluent volumes.\n* Pipette Model: Select which pipette you will use for this protocol.\n* Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n* Plate Type: Select which (destination) plate you will use for this protocol.\n* Reservoir Type: Select which (source) reservoir you will use for this protocol.\n* Filter Tips: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", + "description": "\nConcentration normalization is a key component of many genomic and proteomic applications, such as NGS library prep. With this protocol, you can easily normalize the concentrations of samples in a 96 or 384 microwell plate without worrying about missing a well or adding the wrong volume. Just upload your properly formatted CSV file (keep scrolling for an example), customize your parameters, and download your ready-to-run protocol.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Single-Channel Pipette and corresponding Tips\nSamples in a compatible plate (96-well or 384-well)\nAutomation-friendly reservoir\nDiluent\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nCSV Format\nYour file must be saved as a comma separated value (.csv) file type. Your CSV must contain values corresponding to volumes in microliters (\u03bcL). It should be formatted in \u201clandscape\u201d orientation, with the value corresponding to well A1 in the upper left-hand corner of the value list.\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, and so on.\nIf you\u2019d like to follow our template, you can make a copy of this spreadsheet, fill out your values, and export as CSV from there.\nNote about CSV: All values corresponding to wells in the CSV must have a value (zero (0) is a valid value and nothing will be transferred to the corresponding well(s)). Additionally, the CSV can be formatted in \"portrait\" orientation. In portrait orientation, the bottom left corner is treated as A1 and the top right corner would correspond to the furthest well from A1 (H12 in a 96-well plate).\nUsing the customization fields below, set up your protocol.\n Volumes CSV: Upload the CSV (.csv) containing your diluent volumes.\n Pipette Model: Select which pipette you will use for this protocol.\n Pipette Mount: Specify which mount your single-channel pipette is on (left or right)\n Plate Type: Select which (destination) plate you will use for this protocol.\n Reservoir Type: Select which (source) reservoir you will use for this protocol.\n Filter Tips: Specify whether you want to use filter tips.\n* Tip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.", "internal": "normalization", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/omega-biotek-xpress/README.json b/protoBuilds/omega-biotek-xpress/README.json index a91522f07..8235730f4 100644 --- a/protoBuilds/omega-biotek-xpress/README.json +++ b/protoBuilds/omega-biotek-xpress/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol fully automates the Omega Biotek Mag-Bind Viral RNA XPress Kit. This specific protocol allows the user to manipulate the number of samples, elution volume, as well as tip parking for ultimate reuse (saving up to 4 tip boxes per run).\n\nBefore you begin:\n1. Pre-cool the Temperature Module in the Opentrons App to 4\u00b0C\n2. Create the Binding MasterMix\n\n3. Add the Binding Mastermix, RMP Buffer, Nuclease Free H20, and Lysis Buffer to the 12 well\nreservoir\n4. Create the freshly diluted 80% ethanol and add it to the 1 well reservoir in slot 2\n5. Place the deep well plate filled with samples on top of the magnetic module in slot 4.\n6. Add a 96 well aluminum block and the 96 well PCR plate or PCR strip tubes on top of\nthe Temperature Module in slot 1\nThe final plate of eluates/extractions will be found on top of the temperature module in slot 1.\nExplanation of complex parameters below:\n* Number of Samples: Select the number of samples for this run.\n* Park tips?: if True for \u201ctiprack parking,\u201d tips used for the same buffers with the same samples will be\nreused where 1 tiprack turns into a tiprack where used tips are \u201cparked\u201d. This method has low risk of\ncontamination and is highly recommended to avoid pauses to reuse tips. If selected, the parked tiprack slot is on slot 7.\n* Elution Volume: Specify the elution volume for this run.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", + "description": "This protocol fully automates the Omega Biotek Mag-Bind Viral RNA XPress Kit. This specific protocol allows the user to manipulate the number of samples, elution volume, as well as tip parking for ultimate reuse (saving up to 4 tip boxes per run).\n\nBefore you begin:\n1. Pre-cool the Temperature Module in the Opentrons App to 4\u00b0C\n2. Create the Binding MasterMix\n\n3. Add the Binding Mastermix, RMP Buffer, Nuclease Free H20, and Lysis Buffer to the 12 well\nreservoir\n4. Create the freshly diluted 80% ethanol and add it to the 1 well reservoir in slot 2\n5. Place the deep well plate filled with samples on top of the magnetic module in slot 4.\n6. Add a 96 well aluminum block and the 96 well PCR plate or PCR strip tubes on top of\nthe Temperature Module in slot 1\nThe final plate of eluates/extractions will be found on top of the temperature module in slot 1.\nExplanation of complex parameters below:\n Number of Samples: Select the number of samples for this run.\n Park tips?: if True for \u201ctiprack parking,\u201d tips used for the same buffers with the same samples will be\nreused where 1 tiprack turns into a tiprack where used tips are \u201cparked\u201d. This method has low risk of\ncontamination and is highly recommended to avoid pauses to reuse tips. If selected, the parked tiprack slot is on slot 7.\n Elution Volume: Specify the elution volume for this run.\n P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 multi-channel pipette.\n", "internal": "omega-biotek-xpress", "labware": "NEST 2mL deep well plate (input with samples)\n200\u03bcl filter tip racks (10 x 200\u03bcl if you select false for tiprack parking)\nNEST 1 well reservoir\nNEST 12 well reservoir\nNEST 96 well aluminum block 100ul", "markdown": { diff --git a/protoBuilds/onsite-bms-48plate/README.json b/protoBuilds/onsite-bms-48plate/README.json index 22e50b5cf..6fe386cad 100644 --- a/protoBuilds/onsite-bms-48plate/README.json +++ b/protoBuilds/onsite-bms-48plate/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol transfers sample and diluent to a custom 40 tube rack on the temperature module. Liquid height is tracked in the diluent tube rack, and the temperature module is set to 4C. A fresh tip is granted for each diluent and sample transfer, and mixed after sample is dispensed.\nExplanation of complex parameters below:\n* input .csv file: Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\nDiluent Transfer Volume (ul), Dispense Tube (rack), Source Well, Sample Transfer Volume\n1000, A1, A1, 20\n* Track tips?: Specify whether to start at A1 of both tip racks, or to start picking up from where the last protocol left off.\n* Initial Volume Diluent (mL): Specify the initial volume of diluent in A1 of the 6 tube rack.\n* P20/P1000 Mounts: Specify which mount (left or right) to host the P20 and P1000 pipettes.\n", + "description": "This protocol transfers sample and diluent to a custom 40 tube rack on the temperature module. Liquid height is tracked in the diluent tube rack, and the temperature module is set to 4C. A fresh tip is granted for each diluent and sample transfer, and mixed after sample is dispensed.\nExplanation of complex parameters below:\n input .csv file: Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\nDiluent Transfer Volume (ul), Dispense Tube (rack), Source Well, Sample Transfer Volume\n1000, A1, A1, 20\n Track tips?: Specify whether to start at A1 of both tip racks, or to start picking up from where the last protocol left off.\n Initial Volume Diluent (mL): Specify the initial volume of diluent in A1 of the 6 tube rack.\n P20/P1000 Mounts: Specify which mount (left or right) to host the P20 and P1000 pipettes.\n", "internal": "onsite-bms", "labware": "\nOpentrons 6 Tube Rack with NEST 50 mL Conical\nNEST 96 Well Plate Flat\nOpentrons 20ul Tips\nOpentrons 1000ul Tips\nCustom 40 Tube Rack\n", "markdown": { diff --git a/protoBuilds/onsite-bms/README.json b/protoBuilds/onsite-bms/README.json index 74631d6fa..3da7682bd 100644 --- a/protoBuilds/onsite-bms/README.json +++ b/protoBuilds/onsite-bms/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n", - "description": "This protocol transfers sample and diluent to a custom 40 tube rack on the temperature module. Liquid height is tracked in the diluent tube rack, and the temperature module is set to 4C. A fresh tip is granted for each diluent and sample transfer, and mixed after sample is dispensed.\nExplanation of complex parameters below:\n* input .csv file: Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\nDiluent Transfer Volume (ul), Dispense Tube (rack), Source Well, Sample Transfer Volume\n1000, A1, A1, 20\n* Track tips?: Specify whether to start at A1 of both tip racks, or to start picking up from where the last protocol left off. \n* Initial Volume Diluent (mL): Specify the initial volume of diluent in A1 of the 6 tube rack.\n* P20/P1000 Mounts: Specify which mount (left or right) to host the P20 and P1000 pipettes.\n", + "description": "This protocol transfers sample and diluent to a custom 40 tube rack on the temperature module. Liquid height is tracked in the diluent tube rack, and the temperature module is set to 4C. A fresh tip is granted for each diluent and sample transfer, and mixed after sample is dispensed.\nExplanation of complex parameters below:\n input .csv file: Here, you should upload a .csv file formatted in the following way, being sure to include the header line:\nDiluent Transfer Volume (ul), Dispense Tube (rack), Source Well, Sample Transfer Volume\n1000, A1, A1, 20\n Track tips?: Specify whether to start at A1 of both tip racks, or to start picking up from where the last protocol left off. \n Initial Volume Diluent (mL): Specify the initial volume of diluent in A1 of the 6 tube rack.\n P20/P1000 Mounts: Specify which mount (left or right) to host the P20 and P1000 pipettes.\n", "internal": "onsite-bms", "labware": "\nOpentrons 6 Tube Rack with NEST 50 mL Conical\nNEST 96 Well Plate Flat\nOpentrons 20ul Tips\nOpentrons 1000ul Tips\nCustom 40 Tube Rack\n", "markdown": { diff --git a/protoBuilds/onsite-ganda-1/README.json b/protoBuilds/onsite-ganda-1/README.json index 603162703..661b8e3c6 100644 --- a/protoBuilds/onsite-ganda-1/README.json +++ b/protoBuilds/onsite-ganda-1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nIf the deck layout of a particular protocol is more or less static, it is often helpful to attach a preview of the deck layout, most descriptively generated with Labware Creator. Example:\n\n", - "description": "This is part 1 of a 4 part protocol for the rhAmpSeq kit.\n* Part 2\n\nPart 3\nPart 4\n\nThis portion adds three components to 30 uL samples as outlined in the rhAmpSeq manual.\n* 10X rhAmp PCR Panel - Forward Pool\n* 10X rhAmp PCR Panel - Reverse Pool\n* 4X rhAmpSeq Library Mix 1\nExplanation of complex parameters below:\n* Number of Samples: How many samples are to be run, from 1 to 96\n* P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", + "description": "This is part 1 of a 4 part protocol for the rhAmpSeq kit.\n* Part 2\n\nPart 3\nPart 4\n\nThis portion adds three components to 30 uL samples as outlined in the rhAmpSeq manual.\n 10X rhAmp PCR Panel - Forward Pool\n 10X rhAmp PCR Panel - Reverse Pool\n* 4X rhAmpSeq Library Mix 1\nExplanation of complex parameters below:\n Number of Samples: How many samples are to be run, from 1 to 96\n P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", "internal": "onsite-ganda-lab", "labware": "\nNEST 96 Well Plate\n", "markdown": { diff --git a/protoBuilds/onsite-ganda-2/README.json b/protoBuilds/onsite-ganda-2/README.json index 4bf9a7745..1193231f8 100644 --- a/protoBuilds/onsite-ganda-2/README.json +++ b/protoBuilds/onsite-ganda-2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nFor 96 Samples\n\n", - "description": "This is part 2 of a 4 part protocol for the rhAmpSeq kit.\n* Part 1\n\nPart 3\nPart 4\n\nThis portion performs a cleanup on the PCR amplification product. A reagent list is below:\n* 80% Freshly Prepared Ethanol\n* IDTE Buffer\n* Agencourt AMPure XP Beads\nExplanation of complex parameters below:\n* Number of Samples: How many samples are to be run, from 1 to 96\n* P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", + "description": "This is part 2 of a 4 part protocol for the rhAmpSeq kit.\n* Part 1\n\nPart 3\nPart 4\n\nThis portion performs a cleanup on the PCR amplification product. A reagent list is below:\n 80% Freshly Prepared Ethanol\n IDTE Buffer\n* Agencourt AMPure XP Beads\nExplanation of complex parameters below:\n Number of Samples: How many samples are to be run, from 1 to 96\n P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", "internal": "onsite-ganda-lab", "labware": "\nNEST 96 Well Plate\n", "markdown": { @@ -32,7 +32,7 @@ "pipettes": "\nP20 Multi Gen2\nP300 Multi Gen2\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\n30 uL of Agencourt AMPure XP Beads is added to all samples on the magnetic module in slot 1 and mixed to homogenization\nSamples with beads are incubated for 10 minutes\nThe magnetic module is engaged for 5 minutes\nAn ethanol wash is performed twice as outlined below:\nSupernatant is discarded\n200 uL of 80% ethyl alcohol is added to samples\nSamples are incubated for 1 minute\nSupernatant is discarded\n\n\nRemainder of ethyl alcohol is removed\nSamples are air dried for 3 minutes\nMagnetic module is disengaged\n15 uL of IDTE, ph 8.0 is added to each sample\nSamples are incubated for 3 minutes\nMagnetic module is engaged for 3 minutes\n11 uL of the resulting supernatant is removed to the elution plate in slot 5\nRobot lights flash on and off to signal protocol has completed\n", - "reagent-setup": "\nColor Code:\n\n\n* Reagent Reservoir, Slot 2:\n\n* Reagent Reservoir, Slot 4:\n\n", + "reagent-setup": "\nColor Code:\n\n\n Reagent Reservoir, Slot 2:\n\n Reagent Reservoir, Slot 4:\n\n", "reagents": [ "rhAmpSeq Library Preparation" ], diff --git a/protoBuilds/onsite-ganda-3/README.json b/protoBuilds/onsite-ganda-3/README.json index 4d29f0aa2..52a176ddc 100644 --- a/protoBuilds/onsite-ganda-3/README.json +++ b/protoBuilds/onsite-ganda-3/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This is part 3 of a 4 part protocol for the rhAmpSeq kit.\n* Part 1\n\nPart 2\nPart 4\n\nThis portion adds three components to 30 uL samples as outlined in the rhAmpSeq manual.\n* Indexing PCR Primer i5, prepared in 96 well plate with i7 primer\n* Indexing PCR Primer i7 prepared in 96 well plate with i5 primer\n* 4X rhAmpSeq Library Mix 2\nExplanation of complex parameters below:\n* Number of Samples: How many samples are to be run, from 1 to 96\n* P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", + "description": "This is part 3 of a 4 part protocol for the rhAmpSeq kit.\n* Part 1\n\nPart 2\nPart 4\n\nThis portion adds three components to 30 uL samples as outlined in the rhAmpSeq manual.\n Indexing PCR Primer i5, prepared in 96 well plate with i7 primer\n Indexing PCR Primer i7 prepared in 96 well plate with i5 primer\n* 4X rhAmpSeq Library Mix 2\nExplanation of complex parameters below:\n Number of Samples: How many samples are to be run, from 1 to 96\n P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", "internal": "onsite-ganda-lab", "labware": "\nNEST 96 Well Plate\n", "markdown": { diff --git a/protoBuilds/onsite-ganda-4/README.json b/protoBuilds/onsite-ganda-4/README.json index bad88cec8..8e34c4ea1 100644 --- a/protoBuilds/onsite-ganda-4/README.json +++ b/protoBuilds/onsite-ganda-4/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nFor 96 Samples\n\n", - "description": "This is part 4 of a 4 part protocol for the rhAmpSeq kit.\n* Part 1\n\nPart 2\nPart 3\n\nThis portion performs a cleanup on the PCR amplification product. A reagent list is below:\n* 80% Freshly Prepared Ethanol\n* IDTE Buffer\n* Agencourt AMPure XP Beads\nExplanation of complex parameters below:\n* Number of Samples: How many samples are to be run, from 1 to 96\n* P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", + "description": "This is part 4 of a 4 part protocol for the rhAmpSeq kit.\n* Part 1\n\nPart 2\nPart 3\n\nThis portion performs a cleanup on the PCR amplification product. A reagent list is below:\n 80% Freshly Prepared Ethanol\n IDTE Buffer\n* Agencourt AMPure XP Beads\nExplanation of complex parameters below:\n Number of Samples: How many samples are to be run, from 1 to 96\n P20 Multi GEN2 mount: Which side the P20 Multi pipette is attached to\n* Flash on Protocol Completion?: Will the OT-2 lights flash on and off when the protocol is complete?\n", "internal": "onsite-ganda-lab", "labware": "\nNEST 96 Well Plate\n", "markdown": { @@ -32,7 +32,7 @@ "pipettes": "\nP20 Multi Gen2\nP300 Multi Gen2\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", "protocol-steps": "\n20 uL of Agencourt AMPure XP Beads is added to all samples on the magnetic module in slot 1 and mixed to homogenization\nSamples with beads are incubated for 10 minutes\nThe magnetic module is engaged for 5 minutes\nAn ethanol wash is performed twice as outlined below:\nSupernatant is discarded\n200 uL of 80% ethyl alcohol is added to samples\nSamples are incubated for 1 minute\nSupernatant is discarded\n\n\nRemainder of ethyl alcohol is removed\nSamples are air dried for 3 minutes\nMagnetic module is disengaged\n22 uL of IDTE, ph 8.0 is added to each sample\nSamples are incubated for 3 minutes\nMagnetic module is engaged for 3 minutes\n20 uL of the resulting supernatant is removed to the elution plate in slot 5\nRobot lights flash on and off to signal protocol has completed\n", - "reagent-setup": "\nColor Code:\n\n\n* Reagent Reservoir, Slot 2:\n\n* Reagent Reservoir, Slot 4:\n\n", + "reagent-setup": "\nColor Code:\n\n\n Reagent Reservoir, Slot 2:\n\n Reagent Reservoir, Slot 4:\n\n", "reagents": [ "rhAmpSeq Library Preparation" ], diff --git a/protoBuilds/onsite_atila_nasal/README.json b/protoBuilds/onsite_atila_nasal/README.json index f8a89ebf6..daeb18344 100644 --- a/protoBuilds/onsite_atila_nasal/README.json +++ b/protoBuilds/onsite_atila_nasal/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "\n\nThis protocol preps a 96 well plate with buffer, sample, and mastermix for PCR. See below for details on reagent setup, protocol steps, etc. Tube racks should be placed in order of the slot numbers on the deck, (1, 2, 3,...,7). The pipette will access each tube rack in this order beginning from tube rack 1 on slot 1. The pipettes will access each tuberack by column (A1, B1, C1, A2, B2, C2...), meaning a 94 sample run would have all tube racks in slots 1-6 filled, with 4 tubes in A1, B1, C1, A2 of slot 7.\n\n\nIf running a full plate (94 samples), the protocol will use the multi-channel pipette to dispense mastermix to all 96 wells. For SBM, it will use the multi-channel to dispense into the first 11 columns, and then the single-channel to dispense into the first 6 wells of the 12th column. If running less than 94 samples, say 12 for example, the protocol will use the multi-channel to dispense mastermix and SBM into the first column, then the single channel to dispense to the first four wells of column 2, then finally mastermix and SBM into G12, H12. Note, that extra SBM and mastermix should be placed in wells 1-7 depending on the number of samples.\n\n\nExplanation of complex parameters below:\n* Number of Samples (1-94): Specify the number of samples for this run (1-94).\n* Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate.\n* P20 Single/Multi Pipette Mounts: Specify which mount (left or right) to host each pipette.\n", + "description": "\n\nThis protocol preps a 96 well plate with buffer, sample, and mastermix for PCR. See below for details on reagent setup, protocol steps, etc. Tube racks should be placed in order of the slot numbers on the deck, (1, 2, 3,...,7). The pipette will access each tube rack in this order beginning from tube rack 1 on slot 1. The pipettes will access each tuberack by column (A1, B1, C1, A2, B2, C2...), meaning a 94 sample run would have all tube racks in slots 1-6 filled, with 4 tubes in A1, B1, C1, A2 of slot 7.\n\n\nIf running a full plate (94 samples), the protocol will use the multi-channel pipette to dispense mastermix to all 96 wells. For SBM, it will use the multi-channel to dispense into the first 11 columns, and then the single-channel to dispense into the first 6 wells of the 12th column. If running less than 94 samples, say 12 for example, the protocol will use the multi-channel to dispense mastermix and SBM into the first column, then the single channel to dispense to the first four wells of column 2, then finally mastermix and SBM into G12, H12. Note, that extra SBM and mastermix should be placed in wells 1-7 depending on the number of samples.\n\n\nExplanation of complex parameters below:\n Number of Samples (1-94): Specify the number of samples for this run (1-94).\n Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate.\n* P20 Single/Multi Pipette Mounts: Specify which mount (left or right) to host each pipette.\n", "internal": "atila-nasal", "labware": "\nOpentrons 4-in-1 Tube Racks\nOpentrons 20ul Filter Tips\nCustom 0.12 and 0.2mL 96 well plates\n", "markdown": { diff --git a/protoBuilds/onsite_atila_saliva/README.json b/protoBuilds/onsite_atila_saliva/README.json index f966830b8..a81bfc81d 100644 --- a/protoBuilds/onsite_atila_saliva/README.json +++ b/protoBuilds/onsite_atila_saliva/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "\n\nThis protocol preps a 96 well plate with sample and mastermix for PCR. See below for details on reagent setup, protocol steps, etc. Tube racks should be placed in order of the slot numbers on the deck, (1, 2, 3,...,7). The pipette will access each tube rack in this order beginning from tube rack 1 on slot 1. The pipettes will access each tuberack by column (A1, B1, C1, A2, B2, C2...), meaning a 94 sample run would have all tube racks in slots 1-6 filled, with 4 tubes in A1, B1, C1, A2 of slot 7.\n\n\nIf running a full plate (94 samples), the protocol will use the multi-channel pipette to dispense mastermix to all 96 wells. If running less than 94 samples, say 12 for example, the protocol will use the multi-channel to dispense mastermix into the first column, then the single channel to dispense the first four wells of column 2, then finally mastermix into G12, H12. Note, in this example, that the pipette will be taking mastermix from whichever column it is taking from (1 or 2, dependent on the number of samples running), in which case extra mastermix should be provided for the first four wells of column 1.\n\n\nExplanation of complex parameters below:\n* Number of Samples (1-94): Specify the number of samples for this run (1-94).\n* Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate. \n* P20/P300 Pipette Mounts: Specify which mount (left or right) to host each pipette.\n", + "description": "\n\nThis protocol preps a 96 well plate with sample and mastermix for PCR. See below for details on reagent setup, protocol steps, etc. Tube racks should be placed in order of the slot numbers on the deck, (1, 2, 3,...,7). The pipette will access each tube rack in this order beginning from tube rack 1 on slot 1. The pipettes will access each tuberack by column (A1, B1, C1, A2, B2, C2...), meaning a 94 sample run would have all tube racks in slots 1-6 filled, with 4 tubes in A1, B1, C1, A2 of slot 7.\n\n\nIf running a full plate (94 samples), the protocol will use the multi-channel pipette to dispense mastermix to all 96 wells. If running less than 94 samples, say 12 for example, the protocol will use the multi-channel to dispense mastermix into the first column, then the single channel to dispense the first four wells of column 2, then finally mastermix into G12, H12. Note, in this example, that the pipette will be taking mastermix from whichever column it is taking from (1 or 2, dependent on the number of samples running), in which case extra mastermix should be provided for the first four wells of column 1.\n\n\nExplanation of complex parameters below:\n Number of Samples (1-94): Specify the number of samples for this run (1-94).\n Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate. \n* P20/P300 Pipette Mounts: Specify which mount (left or right) to host each pipette.\n", "internal": "atila-saliva", "labware": "\nOpentrons 4-in-1 Tube Racks\nOpentrons 200ul Filter Tips\nOpentrons 20ul Filter Tips\nCustom 0.12 and 0.2mL 96 well plates\n", "markdown": { diff --git a/protoBuilds/onsite_atila_saliva384_pt1/README.json b/protoBuilds/onsite_atila_saliva384_pt1/README.json index 1d238db64..a208e28c8 100644 --- a/protoBuilds/onsite_atila_saliva384_pt1/README.json +++ b/protoBuilds/onsite_atila_saliva384_pt1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "\nThis protocol reformats 10ul of saliva samples from tubes to a 96 well plate. Tube racks should be placed in order of the slot numbers on the deck, (1, 2, 3,...,7). The pipette will access each tube rack in this order beginning from tube rack 1 on slot 1. The pipettes will access each tuberack by column (A1, B1, C1, A2, B2, C2...), meaning a 94 sample run would have all tube racks in slots 1-6 filled, with 4 tubes in A1, B1, C1, A2 of slot 7.\n\nExplanation of complex parameters below:\n* Number of Samples (1-96): Specify the number of samples for this run (1-96).\n* Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate.\n* P20 Pipette Mount: Specify which mount (left or right) to host the P20 Single-Channel Pipette.\n", + "description": "\nThis protocol reformats 10ul of saliva samples from tubes to a 96 well plate. Tube racks should be placed in order of the slot numbers on the deck, (1, 2, 3,...,7). The pipette will access each tube rack in this order beginning from tube rack 1 on slot 1. The pipettes will access each tuberack by column (A1, B1, C1, A2, B2, C2...), meaning a 94 sample run would have all tube racks in slots 1-6 filled, with 4 tubes in A1, B1, C1, A2 of slot 7.\n\nExplanation of complex parameters below:\n Number of Samples (1-96): Specify the number of samples for this run (1-96).\n Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate.\n* P20 Pipette Mount: Specify which mount (left or right) to host the P20 Single-Channel Pipette.\n", "internal": "atila-saliva-pt1", "labware": "\nOpentrons 4-in-1 Tube Racks\nOpentrons 20ul Filter Tips\nCustom 0.12 and 0.2mL 96 well plates\n", "markdown": { diff --git a/protoBuilds/onsite_atila_saliva384_pt2/README.json b/protoBuilds/onsite_atila_saliva384_pt2/README.json index 413b156fe..cd63c7275 100644 --- a/protoBuilds/onsite_atila_saliva384_pt2/README.json +++ b/protoBuilds/onsite_atila_saliva384_pt2/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Plate 4 (slot 2) should only have 94 samples to allow room for controls. Please refer to the following diagram for how samples are loaded from each of the four quadrants onto the 284 plate with the multi-channel. Any unfilled columns will switch to the single channel. SRM is added to control wells O24 and P24.\n", - "description": "\nThis protocol transfer SRM and saliva sample to a 384 well plate with one mix repetition. 4 plates are loaded into one 384 well plate. If running less than 4 full plates, SRM will still be transferred to the last two wells in the 384 well plate (controls). NOTE: positive and negative controls are to be added manually after the protocol into the last two wells. See below for plate setup.\n\nExplanation of complex parameters below:\n* Number of Samples: Specify the number of samples for each plate.\n* Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate.\n* P20 Pipette Mount: Specify which mount (left or right) to host the P20 Single and Multi-Channel Pipettes.\n", + "description": "\nThis protocol transfer SRM and saliva sample to a 384 well plate with one mix repetition. 4 plates are loaded into one 384 well plate. If running less than 4 full plates, SRM will still be transferred to the last two wells in the 384 well plate (controls). NOTE: positive and negative controls are to be added manually after the protocol into the last two wells. See below for plate setup.\n\nExplanation of complex parameters below:\n Number of Samples: Specify the number of samples for each plate.\n Reaction plate: Specify whether using the non-skirted or half-skirted reaction plate on slot 9. Slot 8 should always use a non-skirted plate.\n* P20 Pipette Mount: Specify which mount (left or right) to host the P20 Single and Multi-Channel Pipettes.\n", "internal": "atila-saliva-pt2", "labware": "\nOpentrons 20ul Filter Tips\nNEST 2mL 96, Deepwell Plate\n", "markdown": { diff --git a/protoBuilds/onsite_galatea_mag_bind/README.json b/protoBuilds/onsite_galatea_mag_bind/README.json index 02648f51e..61f6f3c99 100644 --- a/protoBuilds/onsite_galatea_mag_bind/README.json +++ b/protoBuilds/onsite_galatea_mag_bind/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nTip rack on Slot 1 is used for tip parking if selected.\n\n\n", - "description": "Your OT-2 can fully automate the entire Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below:\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* Binding Buffer Volume: Specify the volume of binding buffer to use (ul).\n* Elution Volume: Specify elution volume (ul).\n* Park Tips: Specify whether to park tips or drop tips.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can fully automate the entire Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below:\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n Binding Buffer Volume: Specify the volume of binding buffer to use (ul).\n Elution Volume: Specify elution volume (ul).\n Park Tips: Specify whether to park tips or drop tips.\n P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "onsite_galatea_mag_bind", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 200uL Filter Tips\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/pcr_prep_part_1/README.json b/protoBuilds/pcr_prep_part_1/README.json index 931653005..daa9012b4 100644 --- a/protoBuilds/pcr_prep_part_1/README.json +++ b/protoBuilds/pcr_prep_part_1/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSlot 1: Option of Opentrons tuberack/tube combo 1, or none\nSlot 2: Option of Opentrons tuberack/tube combo 2, or none\nSlot 3: Choice of Opentrons labware library 12-well reservoir\n\n", - "description": "Part 1 of 2: Master Mix Assembly\nLinks:\n* Part 1: Master Mix Assembly\n* Part 2: Master Mix Distribution and DNA Transfer\nThis protocol allows your robot to create a master mix solution using any reagents stored in one or two different types of tube racks, or reservoir well A2 to A12. The master mix will be created in well A1 of the trough. The ingredient information will be provided as a CSV file. See Additional Notes for more details.\nParameters:\n* right pipette type: Which single channel pipette to use in the right mount\n* left pipette type: Which single channel pipette to use in the left mount\n* Filter or regular tips: Use filter tips or non-filtered.\n* Tuberack 1: Tuberack 1 for reagents (optional)\n* Tuberack 2: Tuberack 2 for reagents (optional)\n* 12-well reservoir: 12 well reservoir for mastermix target and optionally reagents in well A2-A12\n* master mix .csv file: Input csv file (see format below)\n", + "description": "Part 1 of 2: Master Mix Assembly\nLinks:\n Part 1: Master Mix Assembly\n Part 2: Master Mix Distribution and DNA Transfer\nThis protocol allows your robot to create a master mix solution using any reagents stored in one or two different types of tube racks, or reservoir well A2 to A12. The master mix will be created in well A1 of the trough. The ingredient information will be provided as a CSV file. See Additional Notes for more details.\nParameters:\n right pipette type: Which single channel pipette to use in the right mount\n left pipette type: Which single channel pipette to use in the left mount\n Filter or regular tips: Use filter tips or non-filtered.\n Tuberack 1: Tuberack 1 for reagents (optional)\n Tuberack 2: Tuberack 2 for reagents (optional)\n 12-well reservoir: 12 well reservoir for mastermix target and optionally reagents in well A2-A12\n* master mix .csv file: Input csv file (see format below)\n", "internal": "OT-2 PCR Prep v2", "labware": "\n4-in-1 Tube Rack Set\n12-well Trough\n", "markdown": { diff --git a/protoBuilds/pcr_prep_part_2/README.json b/protoBuilds/pcr_prep_part_2/README.json index 1269f4dbd..0b03acb55 100644 --- a/protoBuilds/pcr_prep_part_2/README.json +++ b/protoBuilds/pcr_prep_part_2/README.json @@ -5,7 +5,7 @@ "PCR Prep" ] }, - "description": "Part 2 of 2: Master Mix Distribution and DNA Transfer\nLinks:\n* Part 1: Master Mix Assembly\n* Part 2: Master Mix Distribution and DNA Transfer\nThis protocol allows your robot to distribute a master mix solution from well A1 of a trough to PCR strips. Robot will then transfer DNA samples to the master mix solution.\n\nYou will need:\n* 12-channel reservoir\n* 96-well PCR plate", + "description": "Part 2 of 2: Master Mix Distribution and DNA Transfer\nLinks:\n Part 1: Master Mix Assembly\n Part 2: Master Mix Distribution and DNA Transfer\nThis protocol allows your robot to distribute a master mix solution from well A1 of a trough to PCR strips. Robot will then transfer DNA samples to the master mix solution.\n\nYou will need:\n 12-channel reservoir\n 96-well PCR plate", "internal": "OT-2 PCR Prep v2", "markdown": { "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", diff --git a/protoBuilds/promega-maxwell/README.json b/protoBuilds/promega-maxwell/README.json index 404f0436e..031824655 100644 --- a/protoBuilds/promega-maxwell/README.json +++ b/protoBuilds/promega-maxwell/README.json @@ -31,7 +31,7 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nOpentrons P300 8-Channel Electronic Pipette (GEN2)\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n\nVolumes per reservoir channel: (for 96-sample run, not including dead volume):\n* 9mL of binding buffer\n* 15mL of Wash 1\n* 11mL of Wash 2\n* 11mL of Wash 3\n* 6mL of elution buffer\n", + "reagent-setup": "\nReservoir 1: slot 2\nReservoir 2: slot 3\n\n\nVolumes per reservoir channel: (for 96-sample run, not including dead volume):\n 9mL of binding buffer\n 15mL of Wash 1\n 11mL of Wash 2\n 11mL of Wash 3\n* 6mL of elution buffer\n", "reagents": [ "Promega Maxwell\u00ae HT Viral TNA kit" ], diff --git a/protoBuilds/rem-pcr-plate/README.json b/protoBuilds/rem-pcr-plate/README.json index 439ce32b2..0ffa032e9 100644 --- a/protoBuilds/rem-pcr-plate/README.json +++ b/protoBuilds/rem-pcr-plate/README.json @@ -4,7 +4,7 @@ "PCR Prep": [] }, "deck-setup": "\nAfter each plate is prepared, the protocol pauses, the plate must be removed and the following plate must be placed\n in the same slot.\n \n\n", - "description": "Protocol to dispense master mix (with or without DNA) in PCR plates. The current protocol dispenses only one mix per \nplate. You input the number of plates that you'd like to\nprepare and the protocol pauses after preparing each plate. This gives you the opportunity to wait for the previous \nplate to finish, prepare the following master mix etc. The protocol will tell you which trough you need to pour the mix\ninto for the following plate.\nExplanation of parameters below:\n* Master Mix Source: Do you have one master mix for the whole plate (Reservoir) or one for each row (Plate). NB the\nDeck Setup diagram shows both the Plate and Reservoir (troughs), you only need to put the one\nyou require in place.\n* Number of Plates: The total number of plates you'd like to prepare (one master mix needs to be prepared for each \nplate)\n* Starting Trough: The first trough you'd like to pour the master mix into (e.g. if some troughs have already been\nused). NB the subsequent troughs will be used for the following plates so they also need to be free. Make sure\nthat Number of Plates is not greater than the number of available troughs, if so use a new reservoir plate.\n* Volume to dispense (uL): Typically 9 (without DNA in mix) or 10 (with DNA in mix).\n* Touch Tip on the...: Which side should the tip touch the well on (the opposite side to which you touched the tip\nwhen adding the DNA (if applicable)) \n", + "description": "Protocol to dispense master mix (with or without DNA) in PCR plates. The current protocol dispenses only one mix per \nplate. You input the number of plates that you'd like to\nprepare and the protocol pauses after preparing each plate. This gives you the opportunity to wait for the previous \nplate to finish, prepare the following master mix etc. The protocol will tell you which trough you need to pour the mix\ninto for the following plate.\nExplanation of parameters below:\n Master Mix Source: Do you have one master mix for the whole plate (Reservoir) or one for each row (Plate). NB the\nDeck Setup diagram shows both the Plate and Reservoir (troughs), you only need to put the one\nyou require in place.\n Number of Plates: The total number of plates you'd like to prepare (one master mix needs to be prepared for each \nplate)\n Starting Trough: The first trough you'd like to pour the master mix into (e.g. if some troughs have already been\nused). NB the subsequent troughs will be used for the following plates so they also need to be free. Make sure\nthat Number of Plates is not greater than the number of available troughs, if so use a new reservoir plate.\n Volume to dispense (uL): Typically 9 (without DNA in mix) or 10 (with DNA in mix).\n* Touch Tip on the...: Which side should the tip touch the well on (the opposite side to which you touched the tip\nwhen adding the DNA (if applicable)) \n", "labware": "\nNEST 12 Well Reservoir 15 mL\nShallow Well Plate 200 uL (x2)\n", "markdown": { "author": "[REM Analytics](https://www.remanalytics.ch/)\n\n", diff --git a/protoBuilds/sci-amplex-red/README.json b/protoBuilds/sci-amplex-red/README.json index 73c5a0ab4..411000a64 100644 --- a/protoBuilds/sci-amplex-red/README.json +++ b/protoBuilds/sci-amplex-red/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSlot 3 Temperature Module- Plate initially at 23\u00b0C(deactivated) and after reagent addition, target temperature is 37\u00b0 C.\nSlot 4 Opentrons 96 Filter Tip rack 200\u03bcl\nSlot 5 Opentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap- PMA Dilutions from 10mM to 10\u03bcM.\nSlot 7 Opentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap- Concentrations of H2O2 for standard curve (0.1, 0.2, 0.3, 0.4, 0.5, 1 and 2 \u03bcM) and concentrations of PMA from 0-150 ng/mL\nSlot 10 Opentrons 96 Filter Tip rack 20\u03bcl\nSlot 11 Opentrons 10 Tube Rack with Falcon 4X50 mL, 6X15mL Conical-Rack for holding 5X Reaction buffer, 1X Reaction buffer and Amplex Red Working Reagent\n\n\n\nFigure 1 Deck layout after the reagent additions is carried out.\nSlot 9 A1 tube contains (5X reaction buffer)\nA3 falcon tube contains Distilled water for the 5X reaction buffer dilution. After addition of 5X to the tube, results in 1X Reaction Buffer being present in the same\nB1 contains empty tube in which 1X Reaction buffer, Amplex red dye and HRP are dispensed during the protocol run.\nSlot 7 Opentrons 24 tube rack Eppendorfs A1 to A6 has 20mM,0.0\u03bcM, 0.1\u03bcM,0.2\u03bcM, 0.3\u03bcM, 0.4\u03bcM concentrations of H2O2\nEppendorfs B1 to B6 has 0.5\u03bcM,1\u03bcM 2\u03bcM, 1mM, 100\u03bcM and 20\u03bcM of H2O2\nEppendorfs C1 to D1 have PMA concentrations of 0,10,25,50,75,100 and 150 ng/mL\nrespectively.\nEppendorfs D3, D4 and D5 have reagents 3% H2O2, HRP (Horse Radish Peroxidase) and Amplex red dye respectively\nSlot 5 Opentrons 24 tube rack Eppendorfs from A1 to A3 have PMA concentrations of 1mM,100\u03bcM and 10\u03bcM respectively.\nSlot3 The 96 well plate on the temperature module has the layout where Rows 0 and 2 have different concentrations of H2O2 standards ranging from 0 to 2\u03bcM added to wells (50\u03bcl). The rows 4 to 6 (columns 1 to 7; E1, F1 and G1 have cells which are untreated followed by E2, F2, G2 having cells treated with 10ng/mL of PMA till E7, F7 and G7 being cells treated with 150ng/mL of PMA (50\u03bcl)\n\n\n\nFigure 2 Deck Layout after addition of Amplex red reagent to the 96-well plate that sits on the temperature module (Slot 3).\n\n\n\nFigure 3 This representation shows the addition of 50\u03bcl of Amplex red working solution to the Blank wells A1 and A2 (Figure shows first well A1 containing 1X Reaction Buffer, to which the Amplex red working solution is added). Same steps are followed for the H2O2 standards (Figure shows representative well A9 displaying the addition of Amplex red). Likewise, the steps are same for wells in which THP-1 cells are present and contain different concentrations of PMA (one representative well, E6 is shown above)\n\n", - "description": "This protocol can be used to measure the levels of hydrogen peroxide from THP-1 cells using Amplex Red reagent kit on the OT-2. 96-well plate format is used for this protocol.\nExplanation of complex parameters below:\n* Number of Samples (5-12): Specify the number of samples for this run (from 5 to 12 samples).\n* P300/P20 Mount: Specify which mount (left or right) for the P300 and P20 single channel pipettes. \n", + "description": "This protocol can be used to measure the levels of hydrogen peroxide from THP-1 cells using Amplex Red reagent kit on the OT-2. 96-well plate format is used for this protocol.\nExplanation of complex parameters below:\n Number of Samples (5-12): Specify the number of samples for this run (from 5 to 12 samples).\n P300/P20 Mount: Specify which mount (left or right) for the P300 and P20 single channel pipettes. \n", "internal": "Amplex Red Hydrogen Peroxide Assay", "labware": "\n\nGreiner-Bio One 96-Well White TC plate with clear bottom\n\n\nOpentrons 96 Filter Tip rack 200\u03bcL\n\n\nOpentrons 96 Filter Tip rack 20\u03bcL\n\n\nOpentrons 10 Tube Rack with Falcon 4X50 mL, 6X15mL Conical\n\n\n(2) Opentrons 24 Tube Rack with Eppendorf 1.5 mL Safe-Lock Snapcap\n\n", "markdown": { diff --git a/protoBuilds/sci-dynabeads-tube-1/README.json b/protoBuilds/sci-dynabeads-tube-1/README.json index c45837077..00d8fda0c 100644 --- a/protoBuilds/sci-dynabeads-tube-1/README.json +++ b/protoBuilds/sci-dynabeads-tube-1/README.json @@ -5,7 +5,7 @@ "Thermo Fisher Dynabeads\u2122 Protein A/G" ] }, - "deck-setup": "\n* Beads: 50 uL per sample\n* Antibody: diluted in phosphate-buffered saline with 0.1% Tween 20 (PBS-T), 50 uL per sample ", + "deck-setup": "\n Beads: 50 uL per sample\n Antibody: diluted in phosphate-buffered saline with 0.1% Tween 20 (PBS-T), 50 uL per sample ", "description": "This protocol (Part 1) performs pipetting and mixing of reagents and samples on the OT2 as the first part of automated immunoprecipitation using Thermo Fisher Dynabeads Protein A or Protein G.\nThe user can determine the number of samples to be processed.\nThe samples (e.g. cell lysates), Dynabeads and the antibody specific for the protein of interest will be transferred to and mixed in a 96-well deepwell working plate on the OT2. The first part of the protocol completes at this point allowing the user to move the working plate to an agitation device, an antibody/target protein incubation period determined by the user. After incubation, the process proceeds with the second part of the protocol on the OT2. Dynabeads/antibody/target protein complex will be washed, eluted, and heated to denature. The final product is ready for SDS-PAGE. ", "internal": "sci-dynabeads-tube-1", "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nNEST 1-Well Reservoirs, 195 mL\n4-in-1 Tube Rack Set\nNEST 15 mL Centrifuge Tube\nOpentrons 300\u00b5L Tips\n", diff --git a/protoBuilds/sci-dynabeads-tube-2/README.json b/protoBuilds/sci-dynabeads-tube-2/README.json index 500d04839..8b76ff123 100644 --- a/protoBuilds/sci-dynabeads-tube-2/README.json +++ b/protoBuilds/sci-dynabeads-tube-2/README.json @@ -5,7 +5,7 @@ "Thermo Fisher Dynabeads\u2122 Protein A/G" ] }, - "deck-setup": "\n* Slot 1 - Magnetic module/sample + beads + antibody (red) in 96 deepwell plate (working plate)\n* Slot 2 \u2013 Wash buffer in 12 well reservoir (orange)\n* Slot 3 - Temperature module/96 well PCR plate (final plate)\n* Slot 4 - Tube rack/elution buffer in 15 mL conical tube (purple)\n* Slot 5 \u2013 Tiprack3 (Note: this tiprack is assigned for use in 3 wash steps. The tips are returned to the tiprack and reused and will not be discarded.)\n* Slot 6 \u2013 Tiprack4\n* Slot 7 - Tiprack1\n* Slot 8 - Tiprack2\n* Slot 9 \u2013 Liquid waste", + "deck-setup": "\n Slot 1 - Magnetic module/sample + beads + antibody (red) in 96 deepwell plate (working plate)\n Slot 2 \u2013 Wash buffer in 12 well reservoir (orange)\n Slot 3 - Temperature module/96 well PCR plate (final plate)\n Slot 4 - Tube rack/elution buffer in 15 mL conical tube (purple)\n Slot 5 \u2013 Tiprack3 (Note: this tiprack is assigned for use in 3 wash steps. The tips are returned to the tiprack and reused and will not be discarded.)\n Slot 6 \u2013 Tiprack4\n Slot 7 - Tiprack1\n Slot 8 - Tiprack2\n* Slot 9 \u2013 Liquid waste", "description": "This protocol (Part 2) performs washing and elution on the OT2 as the second part of automated immunoprecipitation using Thermo Fisher Dynabeads Protein A or Protein G.\nThe user can determine the number of samples to be processed.\nThe samples (e.g. cell lysates), Dynabeads and the antibody specific for the protein of interest will be transferred to and mixed in a 96-well deepwell working plate on the OT2. The first part of the protocol completes at this point allowing the user to move the working plate to an agitation device, an antibody/target protein incubation period determined by the user. After incubation, the process proceeds with the second part of the protocol on the OT2. Dynabeads/antibody/target protein complex will be washed, eluted and heated to denature. The final product is ready for SDS-PAGE. ", "internal": "sci-dynabeads-tube-2", "labware": "\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nNEST 1-Well Reservoirs, 195 mL\n4-in-1 Tube Rack Set\nNEST 15 mL Centrifuge Tube\nNEST 12-Well Reservoirs, 15 mL\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\nOpentrons 300\u00b5L Tips\n", diff --git a/protoBuilds/sci-idt-normalase/README.json b/protoBuilds/sci-idt-normalase/README.json index 9cdf2be2d..70caef05d 100644 --- a/protoBuilds/sci-idt-normalase/README.json +++ b/protoBuilds/sci-idt-normalase/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nLeft: Initial Plate Setup, Right: After Moving the Sample plate to Pos 1 and Pooling the samples on a new plate on the\nThermo.\n\nPLATE MOVING\nThe script requires manually transferring the sample plate between the Thermocycler and Magnet. NOTE: In the script\nthe two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of\nthe same labware as the sample plate on the magnet position to calibrate that position.\nREAGENT PLATE\nPrepare the reagents in the Reagent Plate according to the table below. If available, prepare extra volume to account for\noverage. Following the instructions from the IDT Normalase protocols, reagent mixes for Norm II and Inactivation are\nmade for at least 24x samples even if fewer samples are run due to the low volumes.\n\nreagent plate\n\n", - "description": "This is the Normalase protocol that follows the Normalase PCR that is done after the usual fragmentation, End-Repair, A-tailing, and Ligation. The Ligation would have been performed with either a full length adapter ligation using the Normalase Reagent R5, or a stubby universal adapter followed by the barcoded stubby Normalase adapters in the PCR. This protocol follows that modified PCR that can be adapted into other NGS Library preps, before starting the prepared, amplified libraries should be cleaned and quantified, samples must be at least 5ul of 12nM for efficient Normalization. See the IDT Normalase protocol for more information.\nEXAMPLE PROTOCOL SETUP\nThis is an example setup for 24 samples that will be pooled into 3 pools of 8 samples each. The first step is a reaction on the thermocycler, afterwards the plate is transferred to Pos 1 and a new plate for pooled samples and additional reactions goes on the thermocycler. This protocol will pool 5ul of each sample individually with a single channel pipette according to\nthe setup below. The sample setup is configured for 1, 2, or 3 columns of samples into 3 pools, but the configuration can be adjusted for different pooling amounts or number of pools.\n\n\n\n\n\nc setup\n\n\nExplanation of complex parameters below:\n* .CSV File: Provide csv formatted as seen in documentation to specify how many samples per pool is desired. \n* Number of Samples: Specify number of samples for this run.\n* Dry Run: Yes will return tips, skip incubation times, shorten mix, for testing purposes.\n* Use Modules?: Yes will not require modules on the deck and will skip module steps, for testing purposes, if Dry Run is set to Yes, then this variable will automatically set itself to No.\n* Use protocol specific z-offsets?: Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\n* Use NGS Magnetic Block?\": Sets whether there is the Magnetic Block on the Deck (for post-NGS Setup)\n* P20 Single-Channel Mount: Specify which mount (left or right) to mount the P20 single-channel pipette.\n* P20 Multi-Channel Mount: Specify which mount (left or right) to mount the P20 multi-channel pipette.\n", + "description": "This is the Normalase protocol that follows the Normalase PCR that is done after the usual fragmentation, End-Repair, A-tailing, and Ligation. The Ligation would have been performed with either a full length adapter ligation using the Normalase Reagent R5, or a stubby universal adapter followed by the barcoded stubby Normalase adapters in the PCR. This protocol follows that modified PCR that can be adapted into other NGS Library preps, before starting the prepared, amplified libraries should be cleaned and quantified, samples must be at least 5ul of 12nM for efficient Normalization. See the IDT Normalase protocol for more information.\nEXAMPLE PROTOCOL SETUP\nThis is an example setup for 24 samples that will be pooled into 3 pools of 8 samples each. The first step is a reaction on the thermocycler, afterwards the plate is transferred to Pos 1 and a new plate for pooled samples and additional reactions goes on the thermocycler. This protocol will pool 5ul of each sample individually with a single channel pipette according to\nthe setup below. The sample setup is configured for 1, 2, or 3 columns of samples into 3 pools, but the configuration can be adjusted for different pooling amounts or number of pools.\n\n\n\n\n\nc setup\n\n\nExplanation of complex parameters below:\n .CSV File: Provide csv formatted as seen in documentation to specify how many samples per pool is desired. \n Number of Samples: Specify number of samples for this run.\n Dry Run: Yes will return tips, skip incubation times, shorten mix, for testing purposes.\n Use Modules?: Yes will not require modules on the deck and will skip module steps, for testing purposes, if Dry Run is set to Yes, then this variable will automatically set itself to No.\n Use protocol specific z-offsets?: Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\n Use NGS Magnetic Block?\": Sets whether there is the Magnetic Block on the Deck (for post-NGS Setup)\n P20 Single-Channel Mount: Specify which mount (left or right) to mount the P20 single-channel pipette.\n P20 Multi-Channel Mount: Specify which mount (left or right) to mount the P20 multi-channel pipette.\n", "internal": "sci-idt-normalase", "labware": "\n2x Eppendorf 96 well plate full skirt\n1x Nest 96 well plate full skirt\n\n", "markdown": { diff --git a/protoBuilds/sci-idt-xgen-ez/README.json b/protoBuilds/sci-idt-xgen-ez/README.json index 7f8c56821..1d327c5f5 100644 --- a/protoBuilds/sci-idt-xgen-ez/README.json +++ b/protoBuilds/sci-idt-xgen-ez/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs the IDT xGEN EZ kit. This protocol uses the stubby adapter (Reagent W5) that is included in the xGEN EZ kit during ligation and the barcoding of samples is performed during PCR by using either xGEN UDIs or CDIs. The alternate protocol version is IDT xGEN EZ UNI that does the barcoding of samples at ligation instead. The Protocol steps and reagents are different between the two versions. See IDT\u2019s xGEN DNA Library Prep EZ Kit protocol for more information about sample barcode kit requirements.\nExplanation of complex parameters below:\n* Number of Samples: Samples are prepared as pictured below; with 100ng of input DNA in 50ul of Low EDTA. See IDT\u2019s xGEN DNA Library Prep EZ Kit protocol for more information about sample input requirements.\n\n\n* Fragmentation Time (minutes): Minutes, Duration of the Fragmentation Step\n* PCR Cycles: Specify number of PCR cycles if performing PCR on deck.\n* Dry Run: Yes will return tips, skip incubation times, shorten mix, for testing purposes.\n* Use Modules?: Yes will not require modules on the deck and will skip module steps, for testing purposes, if Dry Run is set to Yes, then this variable will automatically set itself to No.\n* Reuse Tips?: No, NYI format for reusing tips\n* Use protocol specific z-offsets?: Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\n* Include Fragmentation / End-Repair / A-Tailing Step?: Specify whether to include this step below. This and all steps below allow you to customize where to start the protocol, run the protocol in parts over multiple days, choose whether to use Opentrons modules or off deck modules, etc.\n* If yes, Fragmentation / End-Repair / A-Tailing on deck or off deck?: Use this step on or off the deck.\n* Include Ligation Step?: Specify whether to include this step in this run.\n* If yes, ligation Step on or off deck?: Use this step on or off the deck.\n* Include Post Ligation Step?: Specify whether to include this step in this run.\n* Include PCR Step?: Specify whether to include this step in this run.\n* If yes, PCR step on or off deck?: Use this step on or off the deck.\n* Include First Post PCR Step?: Specify whether to include this step in this run.\n* Include Second Post PCR Step?: Specify whether to include this step in this run.\n* P20 Multi-Channel Mount: Specify which mount (left or right) to mount the P20 multi-channel pipette.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to mount the P300 multi-channel pipette.\n", + "description": "This protocol performs the IDT xGEN EZ kit. This protocol uses the stubby adapter (Reagent W5) that is included in the xGEN EZ kit during ligation and the barcoding of samples is performed during PCR by using either xGEN UDIs or CDIs. The alternate protocol version is IDT xGEN EZ UNI that does the barcoding of samples at ligation instead. The Protocol steps and reagents are different between the two versions. See IDT\u2019s xGEN DNA Library Prep EZ Kit protocol for more information about sample barcode kit requirements.\nExplanation of complex parameters below:\n Number of Samples: Samples are prepared as pictured below; with 100ng of input DNA in 50ul of Low EDTA. See IDT\u2019s xGEN DNA Library Prep EZ Kit protocol for more information about sample input requirements.\n\n\n Fragmentation Time (minutes): Minutes, Duration of the Fragmentation Step\n PCR Cycles: Specify number of PCR cycles if performing PCR on deck.\n Dry Run: Yes will return tips, skip incubation times, shorten mix, for testing purposes.\n Use Modules?: Yes will not require modules on the deck and will skip module steps, for testing purposes, if Dry Run is set to Yes, then this variable will automatically set itself to No.\n Reuse Tips?: No, NYI format for reusing tips\n Use protocol specific z-offsets?: Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\n Include Fragmentation / End-Repair / A-Tailing Step?: Specify whether to include this step below. This and all steps below allow you to customize where to start the protocol, run the protocol in parts over multiple days, choose whether to use Opentrons modules or off deck modules, etc.\n If yes, Fragmentation / End-Repair / A-Tailing on deck or off deck?: Use this step on or off the deck.\n Include Ligation Step?: Specify whether to include this step in this run.\n If yes, ligation Step on or off deck?: Use this step on or off the deck.\n Include Post Ligation Step?: Specify whether to include this step in this run.\n Include PCR Step?: Specify whether to include this step in this run.\n If yes, PCR step on or off deck?: Use this step on or off the deck.\n Include First Post PCR Step?: Specify whether to include this step in this run.\n Include Second Post PCR Step?: Specify whether to include this step in this run.\n P20 Multi-Channel Mount: Specify which mount (left or right) to mount the P20 multi-channel pipette.\n P300 Multi-Channel Mount: Specify which mount (left or right) to mount the P300 multi-channel pipette.\n", "internal": "sci-idt-xgen-ez", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\n[* NEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons Aluminum Block Set\nOpentrons 20\u00b5L Filter Tips\nOpentrons 200\u00b5L Filter Tips\n", "markdown": { diff --git a/protoBuilds/sci-idt-xgen-mc/README.json b/protoBuilds/sci-idt-xgen-mc/README.json index ce3871df8..dc7bd5895 100644 --- a/protoBuilds/sci-idt-xgen-mc/README.json +++ b/protoBuilds/sci-idt-xgen-mc/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "This protocol performs the IDT xGEN MC kit. This protocol uses the stubby adapter (Reagent L3) that is included in the xGEN MC kit during ligation and the barcoding\nof samples is performed during PCR by using either xGEN UDIs or CDIs. The alternate protocol version is IDT xGEN MC\nUNI that does the barcoding of samples at ligation instead. The Protocol steps and reagents are different between the\ntwo versions. See IDT\u2019s xGEN DNA Library Prep MC Kit protocol for more information about sample barcode kit\nrequirements.\nThe script requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the\nThermocycler and needs to be moved to the Magnet for the post-ligation cleanup, and then moved to the Thermocycler\nfor PCR and then back to the Magnet for the post-PCR cleanup.\nNOTE: In the script the two positions are handled as magnetic sample plate and thermocycler sample plate; during calibration,\nuse an empty plate of the same labware as the sample plate on the magnet position to calibrate that position.\nExplanation of complex parameters below:\n* Number of Samples: Samples are prepared as pictured below; with 100ng of input DNA in 50ul of Low EDTA. See IDT\u2019s xGEN DNA Library Prep EZ Kit protocol for more information about sample input requirements.\n\n\n* PCR Cycles: Specify number of PCR cycles if performing PCR on deck.\n* Dry Run: Yes will return tips, skip incubation times, shorten mix, for testing purposes.\n* Use Modules?: Yes will not require modules on the deck and will skip module steps, for testing purposes, if Dry Run is set to Yes, then this variable will automatically set itself to No.\n* Reuse Tips?: No, NYI format for reusing tips\n* Use protocol specific z-offsets?: Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\n* Include End-Repair / A-Tailing Step?: Specify whether to include this step below. This and all steps below allow you to customize where to start the protocol, run the protocol in parts over multiple days, choose whether to use Opentrons modules or off deck modules, etc.\n* If yes, End-Repair / A-Tailing on deck or off deck?: Use this step on or off the deck.\n* Include Ligation Step?: Specify whether to include this step in this run.\n* If yes, ligation Step on or off deck?: Use this step on or off the deck.\n* Include Post Ligation Step?: Specify whether to include this step in this run.\n* Include PCR Step?: Specify whether to include this step in this run.\n* If yes, PCR step on or off deck?: Use this step on or off the deck.\n* Include First Post PCR Step?: Specify whether to include this step in this run.\n* Include Second Post PCR Step?: Specify whether to include this step in this run.\n* P20 Multi-Channel Mount: Specify which mount (left or right) to mount the P20 multi-channel pipette.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to mount the P300 multi-channel pipette.\n", + "description": "This protocol performs the IDT xGEN MC kit. This protocol uses the stubby adapter (Reagent L3) that is included in the xGEN MC kit during ligation and the barcoding\nof samples is performed during PCR by using either xGEN UDIs or CDIs. The alternate protocol version is IDT xGEN MC\nUNI that does the barcoding of samples at ligation instead. The Protocol steps and reagents are different between the\ntwo versions. See IDT\u2019s xGEN DNA Library Prep MC Kit protocol for more information about sample barcode kit\nrequirements.\nThe script requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the\nThermocycler and needs to be moved to the Magnet for the post-ligation cleanup, and then moved to the Thermocycler\nfor PCR and then back to the Magnet for the post-PCR cleanup.\nNOTE: In the script the two positions are handled as magnetic sample plate and thermocycler sample plate; during calibration,\nuse an empty plate of the same labware as the sample plate on the magnet position to calibrate that position.\nExplanation of complex parameters below:\n Number of Samples: Samples are prepared as pictured below; with 100ng of input DNA in 50ul of Low EDTA. See IDT\u2019s xGEN DNA Library Prep EZ Kit protocol for more information about sample input requirements.\n\n\n PCR Cycles: Specify number of PCR cycles if performing PCR on deck.\n Dry Run: Yes will return tips, skip incubation times, shorten mix, for testing purposes.\n Use Modules?: Yes will not require modules on the deck and will skip module steps, for testing purposes, if Dry Run is set to Yes, then this variable will automatically set itself to No.\n Reuse Tips?: No, NYI format for reusing tips\n Use protocol specific z-offsets?: Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\n Include End-Repair / A-Tailing Step?: Specify whether to include this step below. This and all steps below allow you to customize where to start the protocol, run the protocol in parts over multiple days, choose whether to use Opentrons modules or off deck modules, etc.\n If yes, End-Repair / A-Tailing on deck or off deck?: Use this step on or off the deck.\n Include Ligation Step?: Specify whether to include this step in this run.\n If yes, ligation Step on or off deck?: Use this step on or off the deck.\n Include Post Ligation Step?: Specify whether to include this step in this run.\n Include PCR Step?: Specify whether to include this step in this run.\n If yes, PCR step on or off deck?: Use this step on or off the deck.\n Include First Post PCR Step?: Specify whether to include this step in this run.\n Include Second Post PCR Step?: Specify whether to include this step in this run.\n P20 Multi-Channel Mount: Specify which mount (left or right) to mount the P20 multi-channel pipette.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to mount the P300 multi-channel pipette.\n", "internal": "sci-idt-xgen-mc", "labware": "\nNEST 0.1 mL 96-Well PCR Plate, Full Skirt\n[* NEST 0.1 mL 96-Well PCR Plate, Full Skirt\nNEST 2 mL 96-Well Deep Well Plate, V Bottom\nOpentrons Aluminum Block Set\nOpentrons 20\u00b5L Filter Tips\nOpentrons 200\u00b5L Filter Tips\n\n", "markdown": { @@ -31,6 +31,6 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nP20 Multi-Channel Pipette\nP300 Multi-Channel Pipette\n\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "\nPrepare the reagents in the Reagent Plate according to the table below. If available, prepare extra volume to account for overage. \n\n\n\n* This protocol is designed to be used with xGen UDI Barcode Primers. Add 5ul of the appropriate Barcode adapter to column 7, 8, and 9 according to the experiment design. See IDT xGEN EZ instructions for further details.\n\n* Fill the reservoir wells with the indicated volumes below.\n\n\n* Max Volume is 15ml, refill the EtOH reservoir after the first AMPure Cleanup.\n", + "reagent-setup": "\nPrepare the reagents in the Reagent Plate according to the table below. If available, prepare extra volume to account for overage. \n\n\n\n This protocol is designed to be used with xGen UDI Barcode Primers. Add 5ul of the appropriate Barcode adapter to column 7, 8, and 9 according to the experiment design. See IDT xGEN EZ instructions for further details.\n\n Fill the reservoir wells with the indicated volumes below.\n\n\n* Max Volume is 15ml, refill the EtOH reservoir after the first AMPure Cleanup.\n", "title": "IDT xGEN MC" } \ No newline at end of file diff --git a/protoBuilds/sci-illumina-dna-prep/README.json b/protoBuilds/sci-illumina-dna-prep/README.json index d0989ca75..34007e21c 100644 --- a/protoBuilds/sci-illumina-dna-prep/README.json +++ b/protoBuilds/sci-illumina-dna-prep/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nInital slot layout:\n1. Magnetic module for the sample plate (Nest 96 well plate full skirt).\n2. Reservoir: NEST 12-well reservoir 15 mL. This is substituted for a NEST 2 mL deep well plate if tip-reuse is on in order to minimize cross-contamination. See Reagent Setup section for information about the location of the reagents\n3. Reagent plate 2: Temperature module with Bio-rad 200 \u00b5L plate on aluminum block. See Reagent Setup section for information about the location of the reagents\n4. 20 \u00b5L filter tiprack\n5. 200 \u00b5L filter tiprack\n6. 200 \u00b5L filter tiprack\n7. Sample plate on Thermocycler module with NEST 96 well plate full skirt 100 \u00b5L\n8. Empty\n9. 200 \u00b5L filter tiprack\n10. Sample plate on Thermocycler module with NEST 96 well plate full (thermocycler uses two slots)\n11. Empty", - "description": "This protocol automates the Illumina DNA prep protocol. Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species\nThe protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 \u00b5L of 100 ng:s of sample DNA in each well. See the Illumina DNA Prep protocol for more information about sample input requirements.\n\n\nThe user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below.\nPlate Moving\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\nExplanation of parameters below:\n* Number of samples: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above).\n* Do a dry run?: Sets the Use modules? parameter to No (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes.\n* Use modules?: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to Yes if the Do a dry run? parameter is set to Yes\n* Tip reuse?: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run.\n* Use tip offsets?: Whether to use specific offsets for each tip type\n* Include tagmentation step in protocol run?: Run the tagmentation step or skip it.\n* Run tagmentation incubation on the deck thermocycler?: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler.\n* Run TSB step?: Run the TSB/adapter ligation step or not\n* Run TSB incubation step on the deck thermocycler: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler\n* Run tagmentation wash with TWB step: Run the bead washing steps with TWB\n* Run PCR cycle step: Whether to run the PCR amplification step\n* Run PCR step on deck thermocycler?: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler\n* Run post PCR cleanup step: Run or skip the post-PCR bead cleanup using AMPure beads\n", + "description": "This protocol automates the Illumina DNA prep protocol. Illumina DNA prep offers a fast, integrated workflow for a wide range of applications, from human whole-genome sequencing to amplicons, plasmids, and microbial species\nThe protocol allows you to set the number of samples to 8, 16 or 24 (i.e. 8 samples per column, up to 3 columns). Samples are prepared in the wells as shown in the table and figure below, with 30 \u00b5L of 100 ng:s of sample DNA in each well. See the Illumina DNA Prep protocol for more information about sample input requirements.\n\n\nThe user can choose which steps of the protocol they want to run, or skip - see explanation of parameters below.\nPlate Moving\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-Tagmentation washes, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\nExplanation of parameters below:\n Number of samples: 8 (column 1), 16 (column 1, 3), or 24 (column 1, 3, 5) samples (see above).\n Do a dry run?: Sets the Use modules? parameter to No (see below). Tips will be returned, incubation steps skipped, and mixes shortened. This parameter is for testing purposes.\n Use modules?: Runs the protocol without module steps (e.g. thermocycle steps such as incubation and PCR cycles, or the steps using the magbetic module). Will be automatically set to Yes if the Do a dry run? parameter is set to Yes\n Tip reuse?: Reuses tips for washing steps so that no tip refill is neccesary during the run. Recommended only for a 24x samples run.\n Use tip offsets?: Whether to use specific offsets for each tip type\n Include tagmentation step in protocol run?: Run the tagmentation step or skip it.\n Run tagmentation incubation on the deck thermocycler?: Run the tagmentation incubation step on the deck thermocycler or on an off-deck external thermocycler.\n Run TSB step?: Run the TSB/adapter ligation step or not\n Run TSB incubation step on the deck thermocycler: Whether to do the incubation on the on-deck thermocycler or off-deck on an external thermocycler\n Run tagmentation wash with TWB step: Run the bead washing steps with TWB\n Run PCR cycle step: Whether to run the PCR amplification step\n Run PCR step on deck thermocycler?: Run the PCR amplification on the on-deck thermocycler or on an external thermocycler\n* Run post PCR cleanup step: Run or skip the post-PCR bead cleanup using AMPure beads\n", "internal": "illumina-dna-prep", "labware": "\nNest 96 well plate full skirt 100 \u00b5L\nNEST 2 mL 96-Well Deep Well Plate\nNEST 12-Well Reservoirs, 15 mL\nOpentrons aluminum block set\n", "markdown": { diff --git a/protoBuilds/sci-macherey-nagel-nucleomag/README.json b/protoBuilds/sci-macherey-nagel-nucleomag/README.json index b5d6e03b9..325fb0d42 100644 --- a/protoBuilds/sci-macherey-nagel-nucleomag/README.json +++ b/protoBuilds/sci-macherey-nagel-nucleomag/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nTip rack on Slot 4 is used for tip parking if selected.\n\n", - "description": "Your OT-2 can fully automate the entire NucleoMag\u00ae Virus Viral DNA/RNA Isolation.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below:\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* `: Specify the volume of binding buffer to use (ul).\n*Elution Volume: Specify elution volume (ul).\n*Park Tips: Specify whether to park tips or drop tips.\n*P300 Multi Channel Pipette Mount`: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can fully automate the entire NucleoMag\u00ae Virus Viral DNA/RNA Isolation.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below:\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n* `: Specify the volume of binding buffer to use (ul).\n*Elution Volume: Specify elution volume (ul).\n*Park Tips: Specify whether to park tips or drop tips.\n*P300 Multi Channel Pipette Mount`: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-promega-magazorb-dna-mini-prep-kit", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 200uL Filter Tips\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json b/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json index 5f2bd5045..b74a7c620 100644 --- a/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json +++ b/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nTip rack on Slot 4 is used for tip parking if selected.\n\n", - "description": "Your OT-2 can fully automate the entire Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below:\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* `: Specify the volume of binding buffer to use (ul).\n*Elution Volume: Specify elution volume (ul).\n*Park Tips: Specify whether to park tips or drop tips.\n*P300 Multi Channel Pipette Mount`: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can fully automate the entire Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below:\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n* `: Specify the volume of binding buffer to use (ul).\n*Elution Volume: Specify elution volume (ul).\n*Park Tips: Specify whether to park tips or drop tips.\n*P300 Multi Channel Pipette Mount`: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-mag-bind-blood-tissue-kit", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 200uL Filter Tips\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-neb-next-ultra/README.json b/protoBuilds/sci-neb-next-ultra/README.json index 77b2d2fcf..3d038e534 100644 --- a/protoBuilds/sci-neb-next-ultra/README.json +++ b/protoBuilds/sci-neb-next-ultra/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Please see our guide for a detailed explanation of deck setup. Link to guide", - "description": "This protocol automates the NEBNext\u00ae Ultra\u2122 II DNA Library Prep Kit for Illumina\u00ae on the OT-2.\nThis protocol was developed internally by Opentrons for use on the OT-2 and provides several options. Users can select how many samples to prepare, whether or not to use on-deck modules (like our thermocycler), and whether or not to perform certain steps in the process. Additionally, users can select to enable a \"Test Mode\" that is great for performing a dry run of the protocol.\nFor a more detailed explanation of this protocol, including deck setup and reagent setup, please see this guide: link to guide\nExplanation of complex parameters below:\n* Number of Samples: Select the number of samples to prepare\n* Test Mode (dry run): Select whether to perform a dry run (Yes) instead of a sample run\n* Use Modules: Select whether or not you are using our Magnetic Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/magdeck) and Temperature Module (GEN2)\n* Reuse Tips: Select whether or not to reuse tips for certain steps (selecting yes will reuse tips in a sterile way, saving on the amount of tips used and eliminating the need to replace tips during the run)\n* Use Thermocycler: Select whether or not you will use our on-deck GEN1 thermocycler module. If not using (select \"No\"), the user will be prompted to move the sample plate to an off-deck thermocycler.\n* Use Opentrons Offsets: Select whether to use Z offsets used by the Opentrons Science Team (\"Yes\") or use the default Z heights of the labware (\"No\")\n* Perform ERAT Step: Select whether or not to perform the ERAT step.\n* Perform Ligation Step: Select whether or not to perform the Ligation step.\n* Perform Post-Ligation Step: Select whether or not to perform the Post-Ligtion step.\n* Perform PCR Step: Select whether or not to perform the PCR step.\n* Perform Post-PCR Step: Select whether or not to perform the Post-PCR step.\n", + "description": "This protocol automates the NEBNext\u00ae Ultra\u2122 II DNA Library Prep Kit for Illumina\u00ae on the OT-2.\nThis protocol was developed internally by Opentrons for use on the OT-2 and provides several options. Users can select how many samples to prepare, whether or not to use on-deck modules (like our thermocycler), and whether or not to perform certain steps in the process. Additionally, users can select to enable a \"Test Mode\" that is great for performing a dry run of the protocol.\nFor a more detailed explanation of this protocol, including deck setup and reagent setup, please see this guide: link to guide\nExplanation of complex parameters below:\n Number of Samples: Select the number of samples to prepare\n Test Mode (dry run): Select whether to perform a dry run (Yes) instead of a sample run\n Use Modules: Select whether or not you are using our Magnetic Module (GEN2)](https://shop.opentrons.com/collections/hardware-modules/products/magdeck) and Temperature Module (GEN2)\n Reuse Tips: Select whether or not to reuse tips for certain steps (selecting yes will reuse tips in a sterile way, saving on the amount of tips used and eliminating the need to replace tips during the run)\n Use Thermocycler: Select whether or not you will use our on-deck GEN1 thermocycler module. If not using (select \"No\"), the user will be prompted to move the sample plate to an off-deck thermocycler.\n Use Opentrons Offsets: Select whether to use Z offsets used by the Opentrons Science Team (\"Yes\") or use the default Z heights of the labware (\"No\")\n Perform ERAT Step: Select whether or not to perform the ERAT step.\n Perform Ligation Step: Select whether or not to perform the Ligation step.\n Perform Post-Ligation Step: Select whether or not to perform the Post-Ligtion step.\n Perform PCR Step: Select whether or not to perform the PCR step.\n* Perform Post-PCR Step: Select whether or not to perform the Post-PCR step.\n", "internal": "sci-neb-next-ultra", "labware": "\nNEST 96-Well PCR Plates\nNEST 12-Well Reservoir or NEST 96-Well Deepwell Plate (for more information, please see this guide)\nOpentrons 200\u00b5L Filter Tips\nOpentrons 20\u00b5L Filter Tips\n", "markdown": { diff --git a/protoBuilds/sci-omegabiotek-extraction-fa/README.json b/protoBuilds/sci-omegabiotek-extraction-fa/README.json index 2323a2143..e547713f9 100644 --- a/protoBuilds/sci-omegabiotek-extraction-fa/README.json +++ b/protoBuilds/sci-omegabiotek-extraction-fa/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "After lysing samples, your OT-2 can fully automate the entire Omega Bio-tek Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit. Buffer systems tailored specifically for each type of starting material are added to samples to undergo lysis. Samples are then mixed with HDQ Binding Buffer and Mag-Bind\u00ae Particles HDQ to bind magnetic beads to DNA. DNA is eluted in the Elution Buffer after rapid wash steps.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* Elution Volume: Specify elution volume (ul).\n* Park Tips: Specify whether to park tips or drop tips.\n* Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "After lysing samples, your OT-2 can fully automate the entire Omega Bio-tek Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit. Buffer systems tailored specifically for each type of starting material are added to samples to undergo lysis. Samples are then mixed with HDQ Binding Buffer and Mag-Bind\u00ae Particles HDQ to bind magnetic beads to DNA. DNA is eluted in the Elution Buffer after rapid wash steps.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n Elution Volume: Specify elution volume (ul).\n Park Tips: Specify whether to park tips or drop tips.\n Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-omegabiotek-extraction", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 96 tiprack 300ul\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-omegabiotek-extraction/README.json b/protoBuilds/sci-omegabiotek-extraction/README.json index f4ff44d7c..f3260a78c 100644 --- a/protoBuilds/sci-omegabiotek-extraction/README.json +++ b/protoBuilds/sci-omegabiotek-extraction/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "After lysing samples, your OT-2 can fully automate the entire Omega Bio-tek Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit. Buffer systems tailored specifically for each type of starting material are added to samples to undergo lysis. Samples are then mixed with HDQ Binding Buffer and Mag-Bind\u00ae Particles HDQ to bind magnetic beads to DNA. DNA is eluted in the Elution Buffer after rapid wash steps.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* Elution Volume: Specify elution volume (ul).\n* Park Tips: Specify whether to park tips or drop tips.\n* Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "After lysing samples, your OT-2 can fully automate the entire Omega Bio-tek Mag-Bind\u00ae Blood & Tissue DNA HDQ 96 Kit. Buffer systems tailored specifically for each type of starting material are added to samples to undergo lysis. Samples are then mixed with HDQ Binding Buffer and Mag-Bind\u00ae Particles HDQ to bind magnetic beads to DNA. DNA is eluted in the Elution Buffer after rapid wash steps.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n Elution Volume: Specify elution volume (ul).\n Park Tips: Specify whether to park tips or drop tips.\n Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-omegabiotek-extraction", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 96 tiprack 300ul\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-omegabiotek-magbind-temp/README.json b/protoBuilds/sci-omegabiotek-magbind-temp/README.json index 0f7951617..b9f600a7f 100644 --- a/protoBuilds/sci-omegabiotek-magbind-temp/README.json +++ b/protoBuilds/sci-omegabiotek-magbind-temp/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Tip rack on Slot 5 is used for tip parking if selected. If not tip parking, place 200ul Opentrons Filter Tip Rack in Slot 5.\n", - "description": "Your OT-2 can automate the Mag-Bind\u00ae Viral DNA/RNA 96 Kit. Please see the kit description below found on the [kit website]((https://www.omegabiotek.com/product/mag-bind-viral-dna-rna-96-kit/):\n\"Mag-Bind\u00ae Viral DNA/RNA Kit is designed for the rapid and reliable isolation of viral RNA and viral DNA from serum, swabs, plasma, saliva, and other body fluids. The Mag-Bind\u00ae magnetic beads technology enables purification of high-quality nucleic acids that are free of proteins, nucleases, and other impurities. In addition to easily being adapted with automated systems, this procedure can also be scaled up or down depending on the amount of starting sample. The purified nucleic acids are ready for direct use in downstream applications such as amplification or other enzymatic reactions.\"\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Starting Volume: Specify starting volume of sample (ul).\n* Elution Volume: Specify elution volume (ul).\n* Park Tips: Specify whether to park tips or drop tips.\n* Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can automate the Mag-Bind\u00ae Viral DNA/RNA 96 Kit. Please see the kit description below found on the [kit website]((https://www.omegabiotek.com/product/mag-bind-viral-dna-rna-96-kit/):\n\"Mag-Bind\u00ae Viral DNA/RNA Kit is designed for the rapid and reliable isolation of viral RNA and viral DNA from serum, swabs, plasma, saliva, and other body fluids. The Mag-Bind\u00ae magnetic beads technology enables purification of high-quality nucleic acids that are free of proteins, nucleases, and other impurities. In addition to easily being adapted with automated systems, this procedure can also be scaled up or down depending on the amount of starting sample. The purified nucleic acids are ready for direct use in downstream applications such as amplification or other enzymatic reactions.\"\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Starting Volume: Specify starting volume of sample (ul).\n Elution Volume: Specify elution volume (ul).\n Park Tips: Specify whether to park tips or drop tips.\n Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-omegabiotek-magbind", "labware": "\nNEST 96 Wellplate 2mL\nNEST 1 Reservoir 195mL\nNEST 12 Reservoir 15mL\nOpentrons 96 tiprack 300ul\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json b/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json index 0389fbc4f..e59b81462 100644 --- a/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json +++ b/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSaliva: add 200uL of saliva\nBacteria culture: spin down 200uL of culture, wash once in PBS, resuspend in 200uL of chilled PBS\n200uL of sample + 200uL of lysis buffer. Mix thoroughly, add to deep well plate\nDnase 1 treatment: 49uL of buffer + 1uL of DNAse 1 per sample.\n\n\n", - "description": "Your OT-2 can automate the Mag-Bind\u00ae Viral DNA/RNA 96 Kit. Please see the kit description below found on the kit website:\n\"The Mag-Bind\u00ae Total RNA 96 Kit provides a novel technology for total RNA isolation. This kit allows the rapid and reliable isolation of high-quality total cellular RNA and viral RNA from a wide variety of cells and tissues. Unlike column-based systems, the binding of nucleic acids to magnetic particles occurs in solution resulting in increased binding kinetics and binding efficiency. Particles are also completely re-suspended during the wash steps of the purification protocol, which improves the removal of contaminants and increases nucleic acid purity. Mag-Bind\u00ae Total RNA 96 Kit procedure can be fully automated with most robotic workstations.\"\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* Binding Buffer Volume: Specify binding buffer volume (ul).\n* Wash Volumes: Specify each of the three wash volumes (ul).\n* Elution Volume: Specify elution volume (ul).\n* Settling Time: Specify settling time for beads (minutes).\n* Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n* Park Tips: Specify whether to park tips or drop tips.\n* Track Tips: Specify whether to track tips between runs (starting with fresh tips or pick up from last runs tips).\n* Flash: Specify whether to flash OT-2 lights when the protocol runs out of tips, prompting the user to replenish tips.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can automate the Mag-Bind\u00ae Viral DNA/RNA 96 Kit. Please see the kit description below found on the kit website:\n\"The Mag-Bind\u00ae Total RNA 96 Kit provides a novel technology for total RNA isolation. This kit allows the rapid and reliable isolation of high-quality total cellular RNA and viral RNA from a wide variety of cells and tissues. Unlike column-based systems, the binding of nucleic acids to magnetic particles occurs in solution resulting in increased binding kinetics and binding efficiency. Particles are also completely re-suspended during the wash steps of the purification protocol, which improves the removal of contaminants and increases nucleic acid purity. Mag-Bind\u00ae Total RNA 96 Kit procedure can be fully automated with most robotic workstations.\"\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n Binding Buffer Volume: Specify binding buffer volume (ul).\n Wash Volumes: Specify each of the three wash volumes (ul).\n Elution Volume: Specify elution volume (ul).\n Settling Time: Specify settling time for beads (minutes).\n Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n Park Tips: Specify whether to park tips or drop tips.\n Track Tips: Specify whether to track tips between runs (starting with fresh tips or pick up from last runs tips).\n Flash: Specify whether to flash OT-2 lights when the protocol runs out of tips, prompting the user to replenish tips.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-omegabiotek-magbind-total-rna-96", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 96 tiprack 300ul\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-omegabiotek-magbind/README.json b/protoBuilds/sci-omegabiotek-magbind/README.json index 0f7951617..b9f600a7f 100644 --- a/protoBuilds/sci-omegabiotek-magbind/README.json +++ b/protoBuilds/sci-omegabiotek-magbind/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "Tip rack on Slot 5 is used for tip parking if selected. If not tip parking, place 200ul Opentrons Filter Tip Rack in Slot 5.\n", - "description": "Your OT-2 can automate the Mag-Bind\u00ae Viral DNA/RNA 96 Kit. Please see the kit description below found on the [kit website]((https://www.omegabiotek.com/product/mag-bind-viral-dna-rna-96-kit/):\n\"Mag-Bind\u00ae Viral DNA/RNA Kit is designed for the rapid and reliable isolation of viral RNA and viral DNA from serum, swabs, plasma, saliva, and other body fluids. The Mag-Bind\u00ae magnetic beads technology enables purification of high-quality nucleic acids that are free of proteins, nucleases, and other impurities. In addition to easily being adapted with automated systems, this procedure can also be scaled up or down depending on the amount of starting sample. The purified nucleic acids are ready for direct use in downstream applications such as amplification or other enzymatic reactions.\"\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Starting Volume: Specify starting volume of sample (ul).\n* Elution Volume: Specify elution volume (ul).\n* Park Tips: Specify whether to park tips or drop tips.\n* Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can automate the Mag-Bind\u00ae Viral DNA/RNA 96 Kit. Please see the kit description below found on the [kit website]((https://www.omegabiotek.com/product/mag-bind-viral-dna-rna-96-kit/):\n\"Mag-Bind\u00ae Viral DNA/RNA Kit is designed for the rapid and reliable isolation of viral RNA and viral DNA from serum, swabs, plasma, saliva, and other body fluids. The Mag-Bind\u00ae magnetic beads technology enables purification of high-quality nucleic acids that are free of proteins, nucleases, and other impurities. In addition to easily being adapted with automated systems, this procedure can also be scaled up or down depending on the amount of starting sample. The purified nucleic acids are ready for direct use in downstream applications such as amplification or other enzymatic reactions.\"\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Starting Volume: Specify starting volume of sample (ul).\n Elution Volume: Specify elution volume (ul).\n Park Tips: Specify whether to park tips or drop tips.\n Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-omegabiotek-magbind", "labware": "\nNEST 96 Wellplate 2mL\nNEST 1 Reservoir 195mL\nNEST 12 Reservoir 15mL\nOpentrons 96 tiprack 300ul\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-phytip-plate-prep/README.json b/protoBuilds/sci-phytip-plate-prep/README.json index b52a488bc..fa740817b 100644 --- a/protoBuilds/sci-phytip-plate-prep/README.json +++ b/protoBuilds/sci-phytip-plate-prep/README.json @@ -5,7 +5,7 @@ "Protein A, Pro Plus, Pro Plus LX Columns" ] }, - "deck-setup": "Slot 5 \u2013 96-well V-bottom plate \u2013 1st wash\nSlot 6 - Tiprack1\nSlot 7 - 96-well V-bottom plate - 2nd wash\nSlot 8 \u2013 12-well reagent stock reservoir\n* Green \u2013 equilibration buffer (well #1 and well #2)\n* Blue \u2013 wash buffer 1 (well #3 and well #4)\n* Pink \u2013 wash buffer 2 (well #5 and well #6)\n* Purple \u2013 elution buffer (well #7 and well #8)\nSlot 9 96-well V-bottom plate - equilibration\nSlot 11 - 96-well V-bottom plate - elution\n\n", + "deck-setup": "Slot 5 \u2013 96-well V-bottom plate \u2013 1st wash\nSlot 6 - Tiprack1\nSlot 7 - 96-well V-bottom plate - 2nd wash\nSlot 8 \u2013 12-well reagent stock reservoir\n Green \u2013 equilibration buffer (well #1 and well #2)\n Blue \u2013 wash buffer 1 (well #3 and well #4)\n Pink \u2013 wash buffer 2 (well #5 and well #6)\n Purple \u2013 elution buffer (well #7 and well #8)\nSlot 9 96-well V-bottom plate - equilibration\nSlot 11 - 96-well V-bottom plate - elution\n\n", "description": "This protocol (Plate Prep) performs pipetting to transfer reagents (equilibration buffer, wash buffer 1, wash buffer 2 and elution buffer) from a 12-well reagent stock reservoir to 96-well V-bottom plates (the reagent plates) on the OT-2. These reagent plates are used for the protein purification protocol of Phytip\u00ae Protein A, ProPlus or ProPlus LX Columns.\nThe protocol is developed to prepare sufficient reagents to process up to 96 samples (a full 96-well plate).", "internal": "sci-phytip-plate-prep", "labware": "\nThermo Scientific 96 Well Plate V Bottom 450 uL #249944/249946\nOpentrons 96 Tip Rack 300 \u00b5L\nNEST 12 Well Reservoir 15 mL #360102\nOpentrons Fixed Trash\n", diff --git a/protoBuilds/sci-phytip-protein-A/README.json b/protoBuilds/sci-phytip-protein-A/README.json index 400bc2a0b..4be81b186 100644 --- a/protoBuilds/sci-phytip-protein-A/README.json +++ b/protoBuilds/sci-phytip-protein-A/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSlot 5 \u2013 96-well V-bottom plate \u2013 1st wash\nSlot 6 - Tiprack1\nSlot 7 - 96-well V-bottom plate - 2nd wash\nSlot 8 \u2013 12-well reagent stock reservoir\nGreen \u2013 equilibration buffer (well 1 and well 2)\nBlue \u2013 wash buffer 1 (well 3 and well 4)\nPink \u2013 wash buffer 2 (well 5 and well 6)\nPurple \u2013 elution buffer (well 7 and well 8)\nSlot 9 96-well V-bottom plate - equilibration\nSlot 11 - 96-well V-bottom plate - elution\n\n", - "description": "This protocol (Plate Prep) performs pipetting to transfer reagents (equilibration buffer, wash buffer 1, wash buffer 2 and elution buffer) from a 12-well reagent stock reservoir to 96-well V-bottom plates (the reagent plates) on the OT-2. These reagent plates are used for the protein purification protocol of Phytip\u00ae Protein A, ProPlus or ProPlus LX Columns.\nThe protocol is developed to prepare sufficient reagents to process up to 96 samples (a full 96-well plate).\nExplanation of complex parameters below:\n* Number of Samples: Specify number of samples (1-96) for this run.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel pipette.\n", + "description": "This protocol (Plate Prep) performs pipetting to transfer reagents (equilibration buffer, wash buffer 1, wash buffer 2 and elution buffer) from a 12-well reagent stock reservoir to 96-well V-bottom plates (the reagent plates) on the OT-2. These reagent plates are used for the protein purification protocol of Phytip\u00ae Protein A, ProPlus or ProPlus LX Columns.\nThe protocol is developed to prepare sufficient reagents to process up to 96 samples (a full 96-well plate).\nExplanation of complex parameters below:\n Number of Samples: Specify number of samples (1-96) for this run.\n P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel pipette.\n", "internal": "sci-phytip-protein-A", "labware": "\nThermo Fisher Nunc\u2122 96-Well Polypropylene Storage Microplates\nNEST 12-Well Reservoirs, 15 mL\nOpentrons 300\u00b5L Tips\n", "markdown": { diff --git a/protoBuilds/sci-phytip-protein-puri/README.json b/protoBuilds/sci-phytip-protein-puri/README.json index 9b1b1d6ac..5efa3490c 100644 --- a/protoBuilds/sci-phytip-protein-puri/README.json +++ b/protoBuilds/sci-phytip-protein-puri/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nSlot 2 \u2013 96-well V-bottom plate \u2013 Samples\nSlot 3 - PhyTip\u00ae Columns in an Opentrons 300\u00b5L Tipbox\nSlot 5 \u2013 96-well V-bottom plate \u2013 1st wash\nSlot 7 - 96-well V-bottom plate - 2nd wash\nSlot 9 - 96-well V-bottom plate - equilibration\nSlot 11 - 96-well V-bottom plate - elution\n\n", - "description": "This protocol (Protein Purification) performs protein purification by conducting dual flow chromatography using PhyTip\u00ae Protein A, ProPlus or\nProPlus LX Columns on the OT-2. It is developed to process up to 96 samples (a full 96-well plate).\nExplanation of complex parameters below:\n* Number of Samples: Specify number of samples (1-96) for this run.\n* P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel pipette.\n", + "description": "This protocol (Protein Purification) performs protein purification by conducting dual flow chromatography using PhyTip\u00ae Protein A, ProPlus or\nProPlus LX Columns on the OT-2. It is developed to process up to 96 samples (a full 96-well plate).\nExplanation of complex parameters below:\n Number of Samples: Specify number of samples (1-96) for this run.\n P300 Multi-Channel Mount: Specify which mount (left or right) to host the P300 Multi-Channel pipette.\n", "internal": "sci-phytip-protein-puri", "labware": "\nThermo Fisher Nunc\u2122 96-Well Polypropylene Storage Microplates\nEmpty Opentrons 300\u00b5L Tip Rack for PhyTip\u00ae Columns\n", "markdown": { diff --git a/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/README.json b/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/README.json index 2d067d12b..744538c86 100644 --- a/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/README.json +++ b/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nTip rack on Slot 4 is used for tip parking if selected.\n\n", - "description": "Your OT-2 can fully automate the entire Promega MagaZorb\u00ae DNA Mini-Prep Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* `: Specify the volume of binding buffer to use (ul).\n*Elution Volume: Specify elution volume (ul).\n*Park Tips: Specify whether to park tips or drop tips.\n*P300 Multi Channel Pipette Mount`: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can fully automate the entire Promega MagaZorb\u00ae DNA Mini-Prep Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n* `: Specify the volume of binding buffer to use (ul).\n*Elution Volume: Specify elution volume (ul).\n*Park Tips: Specify whether to park tips or drop tips.\n*P300 Multi Channel Pipette Mount`: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-promega-magazorb-dna-mini-prep-kit", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 200uL Filter Tips\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/sci-roche-hyperprep/README.json b/protoBuilds/sci-roche-hyperprep/README.json index bb5d3aac2..96d85263c 100644 --- a/protoBuilds/sci-roche-hyperprep/README.json +++ b/protoBuilds/sci-roche-hyperprep/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\n\nPosition 1 Magnetic Module\nPosition 2 Reservoir\nPosition 3 Temperature Module w/ Reagent Plate\nPosition 4 p20\nPosition 5 p300\nPosition 6 p300\nPosition 7 Thermocycler Module w/ Sample Plate\n\nPosition 9 p300\n\n\nReservoir w/o Tip Reusing\n\n\nReservoir w/ Tip Reusing\n\n", - "description": "In the script there is a setting definition for the number of samples (SAMPLES = 8x, 16x, or 24x). Samples are prepared as below, with 50ul of 100ng of fragmented sample DNA. See the Roche/KAPA HyperPrep protocol for more information about sample input requirements.\n* \n\n\nPlate Moving\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-ligation cleanup, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\n\n\nTip Tracking\nTip Tracking is an option meant to reuse tips for repeated washes. Instead of discarding tips the OT2 will replace them in their original location for repeated use, this reduces the number of tips needed and allows a 24 sample run to require no tiprack replacements. To prevent cross contamination when reusing Tips, when running the protocol with tip reuse, the reservoir is a 96x 2ml deepwell plate instead of a 12x well 15ml plate. See Reservoir for more details.\n\n\n\nExplanation of complex parameters below:\n* Number of Samples: Specify number of samples 8, 16, or 24.\n* Dry Run: Specify whether performing a dry run or not.\n* Modules or no modules: YES or NO, 'YES' will not require modules on the deck and will skip module steps, for testing purposes, if DRY RUN is 'YES', then NO MODULES will automatically set itself to 'NO'\n* Reuse tips: YES or NO, Reusing tips on wash steps reduces tips needed, no tip refill needed, suggested only for 24x run with all steps\n\nOffset: YES or NO, Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\nInclude ERAT: Steps with \"DECK\" are for reaction to take place with the on deck Thermocycler module. This arrangement makes it possibly to set up and run only the first half, or to skips steps and resume if there is an Error.\nInclude ERAT Deck step: If non \"DECK\" steps are skipped, then TIPREUSE will automatically set\nitself to 'NO' in order to keep tip order correct.\n\n", + "description": "In the script there is a setting definition for the number of samples (SAMPLES = 8x, 16x, or 24x). Samples are prepared as below, with 50ul of 100ng of fragmented sample DNA. See the Roche/KAPA HyperPrep protocol for more information about sample input requirements.\n* \n\n\nPlate Moving\nThe Protocol requires manually transferring the sample plate between the Thermocycler and Magnet 3 times. It starts on the Thermocycler and needs to be moved to the Magnet for the post-ligation cleanup, and then moved to the Thermocycler for PCR and then back to the Magnet for the post-PCR cleanup. In the script the two positions are handled as sample_plate_mag and sample_plate_thermo; during calibration use an empty plate of the same labware as the sample plate on the magnet position to allow calibration.\n\n\nTip Tracking\nTip Tracking is an option meant to reuse tips for repeated washes. Instead of discarding tips the OT2 will replace them in their original location for repeated use, this reduces the number of tips needed and allows a 24 sample run to require no tiprack replacements. To prevent cross contamination when reusing Tips, when running the protocol with tip reuse, the reservoir is a 96x 2ml deepwell plate instead of a 12x well 15ml plate. See Reservoir for more details.\n\n\n\nExplanation of complex parameters below:\n Number of Samples: Specify number of samples 8, 16, or 24.\n Dry Run: Specify whether performing a dry run or not.\n Modules or no modules: YES or NO, 'YES' will not require modules on the deck and will skip module steps, for testing purposes, if DRY RUN is 'YES', then NO MODULES will automatically set itself to 'NO'\n Reuse tips: YES or NO, Reusing tips on wash steps reduces tips needed, no tip refill needed, suggested only for 24x run with all steps\n\nOffset: YES or NO, Sets whether to use protocol specific z offsets for each tip and labware or no offsets aside from defaults\nInclude ERAT: Steps with \"DECK\" are for reaction to take place with the on deck Thermocycler module. This arrangement makes it possibly to set up and run only the first half, or to skips steps and resume if there is an Error.\nInclude ERAT Deck step: If non \"DECK\" steps are skipped, then TIPREUSE will automatically set\nitself to 'NO' in order to keep tip order correct.\n\n", "internal": "sci-roche-hyperprep", "labware": "\nNEST 12 Well Reservoir 195mL\nEppendorf 96 well plate full skirt\nNest 96 well plate full skirt\nOpentrons 20ul Filter Tips\nOpentrons 200ul Filter Tips\n", "markdown": { diff --git a/protoBuilds/sci-thermofisher-magmax/README.json b/protoBuilds/sci-thermofisher-magmax/README.json index af593ab32..86bd1c1d2 100644 --- a/protoBuilds/sci-thermofisher-magmax/README.json +++ b/protoBuilds/sci-thermofisher-magmax/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "Your OT-2 can fully automate the entire Thermofisher MagMAX Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n* park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n* track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n", + "description": "Your OT-2 can fully automate the entire Thermofisher MagMAX Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\nLysed samples should be loaded on the magnetic module in a NEST or USA Scientific 96-deepwell plate. For reagent layout in the 2 12-channel reservoirs used in this protocol, please see \"Setup\" below.\nFor sample traceability and consistency, samples are mapped directly from the magnetic extraction plate (magnetic module, slot 4) to the elution PCR plate (temperature module, slot 1). Magnetic extraction plate well A1 is transferred to elution PCR plate A1, extraction plate well B1 to elution plate B1, ..., D2 to D2, etc.\nExplanation of complex parameters below:\n park tips: If set to yes (recommended), the protocol will conserve tips between reagent addition and removal. Tips will be stored in the wells of an empty rack corresponding to the well of the sample that they access (tip parked in A1 of the empty rack will only be used for sample A1, tip parked in B1 only used for sample B1, etc.). If set to no, tips will always be used only once, and the user will be prompted to manually refill tipracks mid-protocol for high throughput runs.\n track tips across protocol runs: If set to yes, tip racks will be assumed to be in the same state that they were in the previous run. For example, if one completed protocol run accessed tips through column 5 of the 3rd tiprack, the next run will access tips starting at column 6 of the 3rd tiprack. If set to no, tips will be picked up from column 1 of the 1st tiprack.\n* flash: If set to yes, the robot rail lights will flash during any automatic pauses in the protocol. If set to no, the lights will not flash.\n", "internal": "sci-thermofisher-magmax", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 200uL Filter Tips\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { @@ -31,7 +31,7 @@ "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", "pipettes": "\nP300 Multi Channel Pipette\n", "process": "\nInput your protocol parameters above.\nDownload your protocol and unzip if needed.\nUpload your custom labware to the OT App by navigating to More > Custom Labware > Add Labware, and selecting your labware files (.json extensions) if needed.\nUpload your protocol file (.py extension) to the OT App in the Protocol tab.\nSet up your deck according to the deck map.\nCalibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our support articles.\nHit 'Run'.\n", - "reagent-setup": "\nReagents:\n* green: binding buffer\n* pink: wash buffer 1\n* purple: wash buffer 2\n* blue: elution buffer\n* orange: wash buffer 3\n", + "reagent-setup": "\nReagents:\n green: binding buffer\n pink: wash buffer 1\n purple: wash buffer 2\n blue: elution buffer\n* orange: wash buffer 3\n", "reagents": [ "ThermoFisher MagMAX Kit" ], diff --git a/protoBuilds/sci-zymo-directzol-magbead/README.json b/protoBuilds/sci-zymo-directzol-magbead/README.json index d4beb136b..789c4c4c1 100644 --- a/protoBuilds/sci-zymo-directzol-magbead/README.json +++ b/protoBuilds/sci-zymo-directzol-magbead/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "\nTip rack on Slot 4 is used for tip parking if selected.\n\n", - "description": "Your OT-2 can fully automate the entire Zymo Research Direct-zol\u2122-96 MagBead RNA Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\n\nExplanation of complex parameters below:\n* Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n* Deepwell type: Specify which well plate will be mounted on the magnetic module.\n* Reservoir Type: Specify which reservoir will be employed.\n* Starting Volume: Specify starting volume of sample (ul).\n* Elution Volume: Specify elution volume (ul).\n* Park Tips: Specify whether to park tips or drop tips.\n* Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n* P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", + "description": "Your OT-2 can fully automate the entire Zymo Research Direct-zol\u2122-96 MagBead RNA Kit.\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\n\nExplanation of complex parameters below:\n Number of samples: Specify the number of samples this run (1-96 and divisible by 8, i.e. whole columns at a time).\n Deepwell type: Specify which well plate will be mounted on the magnetic module.\n Reservoir Type: Specify which reservoir will be employed.\n Starting Volume: Specify starting volume of sample (ul).\n Elution Volume: Specify elution volume (ul).\n Park Tips: Specify whether to park tips or drop tips.\n Mag Deck Generation: Specify whether GEN1 or GEN2 magnetic module will be used.\n P300 Multi Channel Pipette Mount: Specify whether the P300 multi channel pipette will be on the left or right mount.\n", "internal": "sci-zymo-directzol-magbead", "labware": "\nNEST 96 Wellplate 2mL\nUSA Scientific 96 Wellplate 2.4mL\nNEST 12 Reservoir 15mL\nUSA Scientific 12 Reservoir 22mL\nOpentrons 200uL Filter Tips\nOpentrons 96 Aluminum block Nest Wellplate 100ul\n", "markdown": { diff --git a/protoBuilds/swift-2s-turbo-pt1/README.json b/protoBuilds/swift-2s-turbo-pt1/README.json index 31570b08c..3982c1602 100644 --- a/protoBuilds/swift-2s-turbo-pt1/README.json +++ b/protoBuilds/swift-2s-turbo-pt1/README.json @@ -5,7 +5,7 @@ "NGS Library Prep: Swift 2S Turbo" ] }, - "description": "\nPart 1 of 3: Enzymatic Prep & Ligation\nWith this protocol, your OT-2 can perform the Swift 2S Turbo DNA Library Kit. For more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\nIn this part of the protocol, your OT-2 will complete the enzymatic prep portion and the initial steps of the ligation portion prior to adding your samples to a thermocycler, as described in the Swift 2S Turbo Kit Guide.\nAt the completion of this step, you will add your samples to the thermocycler. Once the thermocycler step is complete, continue with Part 2 of the protocol.\nLinks:\n* Part 1: Enzymatic Prep & Ligation\n* Part 2: Ligation Clean-Up & PCR Prep\n* Part 3: Final Clean-Up\nNote: This workflow replaces the Reagent K2 in the Enzymatic Prep Master Mix with Reagent DE in order to reduce the risk of over fragmentation. For more information, please see this note.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette*\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, resuspended in Low EDTA TE, bringing the total volume to 16\u00b5L\nPCR Strip(s), optional\n\n*Opentrons now sells the P20 Single-Channel Pipette in place of the P50 Single-Channel Pipette. If you have the P50 Single-Channel Pipette, you can use it for this protocol.\nFull setup for the entire protocol:\n\n\n\n\nSpecific to Part 1 of 3\nSlot 1: NEST 96-Well PCR Plate (or PCR Strips) on top of 96-Well Aluminum Block with samples\n* 8 Samples: Column 1\n* 16 Samples: Columns 1 & 2\n* 24 Samples: Columns 1, 2, & 3\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here)\n* A1: Enzymatic Prep Master Mix\n* A2: Ligation Master Mix\n* A3: (used in Part 2) PCR Master Mix\n* B1: (used in Part 2) Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nSlot 5: Opentrons Tips\nUsing the customizations fields, below set up your protocol.\n* Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n* Number of Samples: Specify the number of samples (8, 16 or 24) you'd like to run.", + "description": "\nPart 1 of 3: Enzymatic Prep & Ligation\nWith this protocol, your OT-2 can perform the Swift 2S Turbo DNA Library Kit. For more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\nIn this part of the protocol, your OT-2 will complete the enzymatic prep portion and the initial steps of the ligation portion prior to adding your samples to a thermocycler, as described in the Swift 2S Turbo Kit Guide.\nAt the completion of this step, you will add your samples to the thermocycler. Once the thermocycler step is complete, continue with Part 2 of the protocol.\nLinks:\n Part 1: Enzymatic Prep & Ligation\n Part 2: Ligation Clean-Up & PCR Prep\n* Part 3: Final Clean-Up\nNote: This workflow replaces the Reagent K2 in the Enzymatic Prep Master Mix with Reagent DE in order to reduce the risk of over fragmentation. For more information, please see this note.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette*\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, resuspended in Low EDTA TE, bringing the total volume to 16\u00b5L\nPCR Strip(s), optional\n\n*Opentrons now sells the P20 Single-Channel Pipette in place of the P50 Single-Channel Pipette. If you have the P50 Single-Channel Pipette, you can use it for this protocol.\nFull setup for the entire protocol:\n\n\n\n\nSpecific to Part 1 of 3\nSlot 1: NEST 96-Well PCR Plate (or PCR Strips) on top of 96-Well Aluminum Block with samples\n 8 Samples: Column 1\n 16 Samples: Columns 1 & 2\n* 24 Samples: Columns 1, 2, & 3\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here)\n A1: Enzymatic Prep Master Mix\n A2: Ligation Master Mix\n A3: (used in Part 2) PCR Master Mix\n B1: (used in Part 2) Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nSlot 5: Opentrons Tips\nUsing the customizations fields, below set up your protocol.\n Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n Number of Samples: Specify the number of samples (8, 16 or 24) you'd like to run.", "internal": "Swift-2S-Turbo-pt1", "markdown": { "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", diff --git a/protoBuilds/swift-2s-turbo-pt2/README.json b/protoBuilds/swift-2s-turbo-pt2/README.json index cdc429bcc..f4731eb8c 100644 --- a/protoBuilds/swift-2s-turbo-pt2/README.json +++ b/protoBuilds/swift-2s-turbo-pt2/README.json @@ -5,7 +5,7 @@ "NGS Library Prep: Swift 2S Turbo" ] }, - "description": "\nPart 2 of 3: Ligation Clean-Up & PCR Prep\nWith this protocol, your OT-2 can perform the Swift 2S Turbo DNA Library Kit. For more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\nIn this part of the protocol, your OT-2 will complete the ligation process that was begun in Part 1 and complete the indexing portion up to the thermocycling step (step 18) as outlined in the Swift 2S Turbo Kit Guide.\nAt the completion of this step, you will add your samples to the thermocycler. Once the thermocycler step is complete, continue with Part 3 of the protocol.\nLinks:\n* Part 1: Enzymatic Prep & Ligation\n* Part 2: Ligation Clean-Up & PCR Prep\n* Part 3: Final Clean-Up\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, user collected from Part 1\nPCR Strip(s), optional\n\nFull setup for the entire protocol:\n\n\n\n\nSpecific to Part 2 of 3\nSlot 1: NEST 96-Well PCR Plate (or PCR Strips) on top of 96-Well Aluminum Block with samples the user has collected from Part 1\n* 8 Samples: Column 1\n* 16 Samples: Columns 1 & 2\n* 24 Samples: Columns 1, 2, & 3\nSlot 2: NEST 12-Well Reservoir\n* A1: Magnetic Beads\n* A3: 80% Ethanol Solution, Freshly Prepared\n* A4: 80% Ethanol Solution, Freshly Prepared\n* A6: Low EDTA TE Buffer\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here) and indices (if automating index addition)\n* A1: (used in Part 1) Enzymatic Prep Master Mix\n* A2: (used in Part 1) Ligation Master Mix\n* A3: PCR Master Mix\n* B1: Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nNote: if the user is running 24 samples and chooses to automate indices addition, the robot will pause after addition of the first 16 indices to allow user to replace them with the final 8 indices.\nSlot 4: Opentrons Magnetic Module with NEST 96-Well PCR Plate\nSlot 5: Opentrons Tips for Single-Channel Pipette\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nUsing the customizations fields, below set up your protocol.\n* Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n* P300 8-Channel Pipette Tip Type: Select which tips (filter/non-filter) to be used for this protocol.\n* Number of Samples: Specify the number of samples (8, 16, or 24) you'd like to run.\n* Magdeck Generation: Specify whether using Generation 1 or Generation 2 magdeck.\n* Automate Indexing: Specify whether the indices should be added to the samples with the OT-2, or manually.", + "description": "\nPart 2 of 3: Ligation Clean-Up & PCR Prep\nWith this protocol, your OT-2 can perform the Swift 2S Turbo DNA Library Kit. For more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\nIn this part of the protocol, your OT-2 will complete the ligation process that was begun in Part 1 and complete the indexing portion up to the thermocycling step (step 18) as outlined in the Swift 2S Turbo Kit Guide.\nAt the completion of this step, you will add your samples to the thermocycler. Once the thermocycler step is complete, continue with Part 3 of the protocol.\nLinks:\n Part 1: Enzymatic Prep & Ligation\n Part 2: Ligation Clean-Up & PCR Prep\n* Part 3: Final Clean-Up\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, user collected from Part 1\nPCR Strip(s), optional\n\nFull setup for the entire protocol:\n\n\n\n\nSpecific to Part 2 of 3\nSlot 1: NEST 96-Well PCR Plate (or PCR Strips) on top of 96-Well Aluminum Block with samples the user has collected from Part 1\n 8 Samples: Column 1\n 16 Samples: Columns 1 & 2\n* 24 Samples: Columns 1, 2, & 3\nSlot 2: NEST 12-Well Reservoir\n A1: Magnetic Beads\n A3: 80% Ethanol Solution, Freshly Prepared\n A4: 80% Ethanol Solution, Freshly Prepared\n A6: Low EDTA TE Buffer\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here) and indices (if automating index addition)\n A1: (used in Part 1) Enzymatic Prep Master Mix\n A2: (used in Part 1) Ligation Master Mix\n A3: PCR Master Mix\n B1: Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nNote: if the user is running 24 samples and chooses to automate indices addition, the robot will pause after addition of the first 16 indices to allow user to replace them with the final 8 indices.\nSlot 4: Opentrons Magnetic Module with NEST 96-Well PCR Plate\nSlot 5: Opentrons Tips for Single-Channel Pipette\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nUsing the customizations fields, below set up your protocol.\n Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n P300 8-Channel Pipette Tip Type: Select which tips (filter/non-filter) to be used for this protocol.\n Number of Samples: Specify the number of samples (8, 16, or 24) you'd like to run.\n Magdeck Generation: Specify whether using Generation 1 or Generation 2 magdeck.\n* Automate Indexing: Specify whether the indices should be added to the samples with the OT-2, or manually.", "internal": "Swift-2S-Turbo-pt2", "markdown": { "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", diff --git a/protoBuilds/swift-2s-turbo-pt3/README.json b/protoBuilds/swift-2s-turbo-pt3/README.json index d0ffb107d..101018be1 100644 --- a/protoBuilds/swift-2s-turbo-pt3/README.json +++ b/protoBuilds/swift-2s-turbo-pt3/README.json @@ -5,7 +5,7 @@ "NGS Library Prep: Swift 2S Turbo" ] }, - "description": "\nPart 3 of 3: Final Clean-Up\nWith this protocol, your OT-2 can perform the Swift 2S Turbo DNA Library Kit. For more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\nIn this part of the protocol, your OT-2 will complete the final bead clean-up of the protocol as outlined in the Swift 2S Turbo Kit Guide.\nAt the completion of this step, you will have 20\u03bcl of elution from each sample that contains the final library.\nLinks:\n* Part 1: Enzymatic Prep & Ligation\n* Part 2: Ligation Clean-Up & PCR Prep\n* Part 3: Final Clean-Up\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, user collected from Part 2\nPCR Strip(s), optional\n\nFull setup for the entire protocol:\n\n\n\n\nSpecific to Part 3 of 3\nSlot 1: NEST 96-Well PCR Plate (or PCR Strips) on top of 96-Well Aluminum Block with samples the user has collected from Part 2\n* 8 Samples: Column 4\n* 16 Samples: Columns 4 & 5\n* 24 Samples: Columns 4, 5, & 6\nSlot 2: NEST 12-Well Reservoir\n* A1: Magnetic Beads\n* A4: 80% Ethanol Solution, Freshly Prepared\n* A6: Low EDTA TE Buffer\nSlot 4: Opentrons Magnetic Module with NEST 96-Well PCR Plate\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nUsing the customizations fields, below set up your protocol.\n* P300 8-Channel Pipette Tip Type: Select which tips (filter/non-filter) to be used for this protocol.\n* Number of Samples: Specify the number of samples (8, 16, or 24) you'd like to run.\n* Magdeck Generation: Specify whether using Generation 1 or Generation 2 magdeck. \nNote: The final elution will be transferred to column 7 (and column 8 and column 9, if running 16 samples or 24 samples, respectively) of the PCR plate (or strips) in slot 1.", + "description": "\nPart 3 of 3: Final Clean-Up\nWith this protocol, your OT-2 can perform the Swift 2S Turbo DNA Library Kit. For more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\nIn this part of the protocol, your OT-2 will complete the final bead clean-up of the protocol as outlined in the Swift 2S Turbo Kit Guide.\nAt the completion of this step, you will have 20\u03bcl of elution from each sample that contains the final library.\nLinks:\n Part 1: Enzymatic Prep & Ligation\n Part 2: Ligation Clean-Up & PCR Prep\n* Part 3: Final Clean-Up\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, user collected from Part 2\nPCR Strip(s), optional\n\nFull setup for the entire protocol:\n\n\n\n\nSpecific to Part 3 of 3\nSlot 1: NEST 96-Well PCR Plate (or PCR Strips) on top of 96-Well Aluminum Block with samples the user has collected from Part 2\n 8 Samples: Column 4\n 16 Samples: Columns 4 & 5\n* 24 Samples: Columns 4, 5, & 6\nSlot 2: NEST 12-Well Reservoir\n A1: Magnetic Beads\n A4: 80% Ethanol Solution, Freshly Prepared\n* A6: Low EDTA TE Buffer\nSlot 4: Opentrons Magnetic Module with NEST 96-Well PCR Plate\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nUsing the customizations fields, below set up your protocol.\n P300 8-Channel Pipette Tip Type: Select which tips (filter/non-filter) to be used for this protocol.\n Number of Samples: Specify the number of samples (8, 16, or 24) you'd like to run.\n* Magdeck Generation: Specify whether using Generation 1 or Generation 2 magdeck. \nNote: The final elution will be transferred to column 7 (and column 8 and column 9, if running 16 samples or 24 samples, respectively) of the PCR plate (or strips) in slot 1.", "internal": "Swift-2S-Turbo-pt3", "markdown": { "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", diff --git a/protoBuilds/swift-fully-automated-custom/README.json b/protoBuilds/swift-fully-automated-custom/README.json index a6047bcc8..0fd2d6e92 100644 --- a/protoBuilds/swift-fully-automated-custom/README.json +++ b/protoBuilds/swift-fully-automated-custom/README.json @@ -5,7 +5,7 @@ "Swift 2S Turbo" ] }, - "description": "\nThis protocol is a custom modification to the Swift 2S Turbo DNA Library Kit Protocol: Fully Automated already found in the Opentrons Protocol Library. This version of the protocol features lowers aspiration flow rates to avoid bead pick-up, longer incubation times, and less volume of supernatant removed. This version also features both generations of the magnetic module. If running 24 samples with this protocol, the protocol will stop when it runs out of tips, prompting the user to replace tip racks.\nWith this protocol, your OT-2 can fully automate the entire Swift 2S Turbo DNA Library Kit. Simply press start and your OT-2 can automate this entire workflow without any hands-on requirement - from enzymatic prep to sequence ready libraries! Up to 16 libraries can be prepared in under 3 hours.\nFor more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\n\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Thermocycler Module\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette*\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, resuspended in Low EDTA TE, bringing the total volume to 19.5\u00b5L\n\n*Opentrons now sells the P20 Single-Channel Pipette in place of the P50 Single-Channel Pipette. If you have the P50 Single-Channel Pipette, you can use it for this protocol.\nFull setup for the entire protocol:\n\n\n\n\nSlot 1: NEST 96-Well PCR Plate on Opentrons Magnetic Module\nSlot 2: NEST 12-Well Reservoir with Reagents\n* A2: Magnetic Beads; recommended volume: 3-4mL, 4-5mL if running 24 samples.\n* A3: 80% Ethanol Solution, Freshly Prepared; recommended volume: 9-10mL, max allowable reservoir well volume if running 24 samples (watch for overflowing if the multi-channel pipette dunks).\n* A4: 80% Ethanol Solution, Freshly Prepared (if running 16 samples); recommended volume: 9-10mL, max allowable reservoir well volume if running 24 samples (watch for overflowing if the multi-channel pipette dunks).\n* A6: Low EDTA TE Buffer; recommended volume: ~3mL\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here) and indices (if automating index addition)\n* A1: Enzymatic Prep Master Mix\n* A2: Ligation Master Mix\n* A3: PCR Master Mix\n* B1: Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nSlot 4: Opentrons Tips for Single-Channel Pipette\nSlot 5: Opentrons Tips for P300 8-Channel Pipette\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nSlot 7/8/10/11: Opentrons Thermocycler Module with samples in a NEST 96-Well PCR Plate\n* 8 Samples: Column 1\n* 16 Samples: Columns 1 & 2\nUsing the customizations fields, below set up your protocol.\n* Number of Samples: Specify the number of samples (8, 16, 24) you'd like to run.\n* Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n* P300 8-Channel Pipette Tip Type: Select which tips (Filter/Non-Filter) for P300 8-Channel Pipette\n* Automate Indexing: Specify whether the indices should be added to the samples with the OT-2, or manually.\n* Number of PCR Cycles: See suggested cycles here. See Swift 2S Turbo manual for more detailed information.\n* Fragmentation Time: Fragmentation time varies depending on 1) Lot number of the kit and 2) whether the desired insert size is 200bp or 350bp. Please refer to the manual and Lot number on your kit for more information.\nNote: The final 20\u00b5L elution will be transferred to Column 3 if running 8 samples, Columns 5 & 6 if running 16 samples, and Columns 5, 6, and 7 if running 24 samples of the PCR plate on the Thermocycler", + "description": "\nThis protocol is a custom modification to the Swift 2S Turbo DNA Library Kit Protocol: Fully Automated already found in the Opentrons Protocol Library. This version of the protocol features lowers aspiration flow rates to avoid bead pick-up, longer incubation times, and less volume of supernatant removed. This version also features both generations of the magnetic module. If running 24 samples with this protocol, the protocol will stop when it runs out of tips, prompting the user to replace tip racks.\nWith this protocol, your OT-2 can fully automate the entire Swift 2S Turbo DNA Library Kit. Simply press start and your OT-2 can automate this entire workflow without any hands-on requirement - from enzymatic prep to sequence ready libraries! Up to 16 libraries can be prepared in under 3 hours.\nFor more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\n\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Thermocycler Module\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette*\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, resuspended in Low EDTA TE, bringing the total volume to 19.5\u00b5L\n\n*Opentrons now sells the P20 Single-Channel Pipette in place of the P50 Single-Channel Pipette. If you have the P50 Single-Channel Pipette, you can use it for this protocol.\nFull setup for the entire protocol:\n\n\n\n\nSlot 1: NEST 96-Well PCR Plate on Opentrons Magnetic Module\nSlot 2: NEST 12-Well Reservoir with Reagents\n A2: Magnetic Beads; recommended volume: 3-4mL, 4-5mL if running 24 samples.\n A3: 80% Ethanol Solution, Freshly Prepared; recommended volume: 9-10mL, max allowable reservoir well volume if running 24 samples (watch for overflowing if the multi-channel pipette dunks).\n A4: 80% Ethanol Solution, Freshly Prepared (if running 16 samples); recommended volume: 9-10mL, max allowable reservoir well volume if running 24 samples (watch for overflowing if the multi-channel pipette dunks).\n A6: Low EDTA TE Buffer; recommended volume: ~3mL\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here) and indices (if automating index addition)\n A1: Enzymatic Prep Master Mix\n A2: Ligation Master Mix\n A3: PCR Master Mix\n B1: Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nSlot 4: Opentrons Tips for Single-Channel Pipette\nSlot 5: Opentrons Tips for P300 8-Channel Pipette\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nSlot 7/8/10/11: Opentrons Thermocycler Module with samples in a NEST 96-Well PCR Plate\n 8 Samples: Column 1\n 16 Samples: Columns 1 & 2\nUsing the customizations fields, below set up your protocol.\n Number of Samples: Specify the number of samples (8, 16, 24) you'd like to run.\n Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n P300 8-Channel Pipette Tip Type: Select which tips (Filter/Non-Filter) for P300 8-Channel Pipette\n Automate Indexing: Specify whether the indices should be added to the samples with the OT-2, or manually.\n Number of PCR Cycles: See suggested cycles here. See Swift 2S Turbo manual for more detailed information.\n Fragmentation Time: Fragmentation time varies depending on 1) Lot number of the kit and 2) whether the desired insert size is 200bp or 350bp. Please refer to the manual and Lot number on your kit for more information.\nNote: The final 20\u00b5L elution will be transferred to Column 3 if running 8 samples, Columns 5 & 6 if running 16 samples, and Columns 5, 6, and 7 if running 24 samples of the PCR plate on the Thermocycler", "internal": "swift-fully-automated-custom", "markdown": { "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", diff --git a/protoBuilds/swift-fully-automated/README.json b/protoBuilds/swift-fully-automated/README.json index 97600c0f6..d3b3a4d5f 100644 --- a/protoBuilds/swift-fully-automated/README.json +++ b/protoBuilds/swift-fully-automated/README.json @@ -5,7 +5,7 @@ "Swift 2S Turbo" ] }, - "description": "\nWith this protocol, your OT-2 can fully automate the entire Swift 2S Turbo DNA Library Kit. Simply press start and your OT-2 can automate this entire workflow without any hands-on requirement - from enzymatic prep to sequence ready libraries! Up to 16 libraries can be prepared in under 3 hours.\nFor more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\n\nUpdate (April 12, 2021): This protocol has been updated to fix an issue with the final elution destination when selecting 16 samples.\nUpdate (April 13, 2021): This protocol has been updated to accommodate the GEN2 Magnetic Module and fix an issue when using 200\u00b5L filter tips.\nUpdate (September 2, 2021): This protocol has been updated to allow for the GEN2 P300 8-Channel Pipette and has fixed an issue when using 16 samples that caused the 8-channel pipette to go to the wrong source wells during step 1220.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Thermocycler Module\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette*\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, resuspended in Low EDTA TE, bringing the total volume to 19.5\u00b5L\n\n*Opentrons now sells the P20 Single-Channel Pipette in place of the P50 Single-Channel Pipette. If you have the P50 Single-Channel Pipette, you can use it for this protocol.\nFull setup for the entire protocol:\n\n\n\n\nSlot 1: NEST 96-Well PCR Plate on Opentrons Magnetic Module\nSlot 2: NEST 12-Well Reservoir with Reagents\n* A2: Magnetic Beads; recommended volume: 3-4mL\n* A3: 80% Ethanol Solution, Freshly Prepared; recommended volume: 9-10mL\n* A4: 80% Ethanol Solution, Freshly Prepared (if running 16 samples); recommended volume: 9-10mL\n* A6: Low EDTA TE Buffer; recommended volume: 3mL\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here) and indices (if automating index addition)\n* A1: Enzymatic Prep Master Mix\n* A2: Ligation Master Mix\n* A3: PCR Master Mix\n* B1: Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nSlot 4: Opentrons Tips for Single-Channel Pipette\nSlot 5: Opentrons Tips for P300 8-Channel Pipette\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nSlot 7/8/10/11: Opentrons Thermocycler Module with samples in a NEST 96-Well PCR Plate\n* 8 Samples: Column 1\n* 16 Samples: Columns 1 & 2\nUsing the customizations fields, below set up your protocol.\n* Number of Samples: Specify the number of samples (8 or 16) you'd like to run.\n* Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n* P300 8-Channel Pipette Tip Type: Select which tips (Filter/Non-Filter) for P300 8-Channel Pipette\n* Automate Indexing: Specify whether the indices should be added to the samples with the OT-2, or manually.\n* Number of PCR Cycles: See suggested cycles here. See Swift 2S Turbo manual for more detailed information.\n* Fragmentation Time: Fragmentation time varies depending on 1) Lot number of the kit and 2) whether the desired insert size is 200bp or 350bp. Please refer to the manual and Lot number on your kit for more information.\nNote: The final 20\u00b5L elution will be transferred to Column 3 if running 8 samples or Columns 5 & 6 if running 16 samples of the PCR plate on the Thermocycler", + "description": "\nWith this protocol, your OT-2 can fully automate the entire Swift 2S Turbo DNA Library Kit. Simply press start and your OT-2 can automate this entire workflow without any hands-on requirement - from enzymatic prep to sequence ready libraries! Up to 16 libraries can be prepared in under 3 hours.\nFor more information about the Swift 2S Turbo Kit and the Swift 2S Turbo Unique Dual Indexing Primer Kit on the OT-2, please see our Application Note here: Rapid high quality next generation sequencing library preparation with Swift 2S Turbo DNA Library Kits on the Opentrons OT-2\n\nUpdate (April 12, 2021): This protocol has been updated to fix an issue with the final elution destination when selecting 16 samples.\nUpdate (April 13, 2021): This protocol has been updated to accommodate the GEN2 Magnetic Module and fix an issue when using 200\u00b5L filter tips.\nUpdate (September 2, 2021): This protocol has been updated to allow for the GEN2 P300 8-Channel Pipette and has fixed an issue when using 16 samples that caused the 8-channel pipette to go to the wrong source wells during step 1220.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\nAttention: You can now purchase all of the consumables needed to run this protocol by clicking here.\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nSwift 2S Turbo DNA Library Kit\nSwift 2S Turbo Unique Dual Indexing Primer Kit\nOmega Mag-Bind TotalPure NGS Kit\nOpentrons Thermocycler Module\nOpentrons Temperature Module with Aluminum Block Set\nOpentrons Magnetic Module\nOpentrons P20 Single-Channel Pipette or Opentrons P50 Single-Channel Pipette*\nOpentrons P300 Multi-Channel Pipette\nOpentrons Tips\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 2mL Tubes\nSamples, resuspended in Low EDTA TE, bringing the total volume to 19.5\u00b5L\n\n*Opentrons now sells the P20 Single-Channel Pipette in place of the P50 Single-Channel Pipette. If you have the P50 Single-Channel Pipette, you can use it for this protocol.\nFull setup for the entire protocol:\n\n\n\n\nSlot 1: NEST 96-Well PCR Plate on Opentrons Magnetic Module\nSlot 2: NEST 12-Well Reservoir with Reagents\n A2: Magnetic Beads; recommended volume: 3-4mL\n A3: 80% Ethanol Solution, Freshly Prepared; recommended volume: 9-10mL\n A4: 80% Ethanol Solution, Freshly Prepared (if running 16 samples); recommended volume: 9-10mL\n A6: Low EDTA TE Buffer; recommended volume: 3mL\nSlot 3: Opentrons Temperature Module with 24-Well Aluminum Block and NEST 2mL Tubes with master mixes (for more information on master mixes, click here) and indices (if automating index addition)\n A1: Enzymatic Prep Master Mix\n A2: Ligation Master Mix\n A3: PCR Master Mix\n B1: Indexing Reagent 1 (in original container); loaded sequentially (Reagent 2 - B2; Reagent 3 - B3...)\nSlot 4: Opentrons Tips for Single-Channel Pipette\nSlot 5: Opentrons Tips for P300 8-Channel Pipette\nSlot 6: Opentrons Tips for P300 8-Channel Pipette\nSlot 9: Opentrons Tips for P300 8-Channel Pipette\nSlot 7/8/10/11: Opentrons Thermocycler Module with samples in a NEST 96-Well PCR Plate\n 8 Samples: Column 1\n 16 Samples: Columns 1 & 2\nUsing the customizations fields, below set up your protocol.\n Number of Samples: Specify the number of samples (8 or 16) you'd like to run.\n Pipette and Tip Type: Select which pipette (P50 Single-Channel or P20 Single-Channel) and corresponding tips to be used for this protocol. The pipette should be attached to the left mount.\n P300 8-Channel Pipette Tip Type: Select which tips (Filter/Non-Filter) for P300 8-Channel Pipette\n Automate Indexing: Specify whether the indices should be added to the samples with the OT-2, or manually.\n Number of PCR Cycles: See suggested cycles here. See Swift 2S Turbo manual for more detailed information.\n Fragmentation Time: Fragmentation time varies depending on 1) Lot number of the kit and 2) whether the desired insert size is 200bp or 350bp. Please refer to the manual and Lot number on your kit for more information.\nNote: The final 20\u00b5L elution will be transferred to Column 3 if running 8 samples or Columns 5 & 6 if running 16 samples of the PCR plate on the Thermocycler", "internal": "swift-fully-automated", "markdown": { "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", diff --git a/protoBuilds/testdrive/README.json b/protoBuilds/testdrive/README.json index 0419016e6..93ad8f13d 100644 --- a/protoBuilds/testdrive/README.json +++ b/protoBuilds/testdrive/README.json @@ -6,7 +6,7 @@ ] }, "deck-setup": "", - "description": "Learn the OT-2 in under 10 minutes! This protocol will walk you through most of the OT-2 capabilities which include but are not limited to: touch tip, blow out, return tip, and distribute functions (for all functions covered in this protocol, see Protocol Steps section below). \nUnderstand what each OT-2 function does, and see it in real time before incorporating it into your own biology workflow.\nExplanation of complex parameters below:\n* Well Plate: Select which well plate will be loaded onto the deck.\n* Pipette: Select which single-channel pipette will be loaded onto the deck.\n* Pipette Tips: Select which pipette tips will accommodate the pipette you selected above.\nPipette Mount: Select which mount your pipette will be hosted on.\n", + "description": "Learn the OT-2 in under 10 minutes! This protocol will walk you through most of the OT-2 capabilities which include but are not limited to: touch tip, blow out, return tip, and distribute functions (for all functions covered in this protocol, see Protocol Steps section below). \nUnderstand what each OT-2 function does, and see it in real time before incorporating it into your own biology workflow.\nExplanation of complex parameters below:\n Well Plate: Select which well plate will be loaded onto the deck.\n Pipette: Select which single-channel pipette will be loaded onto the deck.\n* Pipette Tips: Select which pipette tips will accommodate the pipette you selected above.\nPipette Mount: Select which mount your pipette will be hosted on.\n", "internal": "testdrive", "labware": "\nAll well plates found in our labware library can be used in this protocol.\nAll Opentrons tip racks found in our labware library can be used in this protocol.\n", "markdown": { diff --git a/protoBuilds/thermocycler/README.json b/protoBuilds/thermocycler/README.json index 9d2ae2be2..cd9d85ad7 100644 --- a/protoBuilds/thermocycler/README.json +++ b/protoBuilds/thermocycler/README.json @@ -5,7 +5,7 @@ "Thermocycler Example" ] }, - "description": "This is a demo protocol, intended for using the Opentrons Thermocycler Module as a thermocycler. This protocol does not involve any liquid handling, so no pipettes are required to run this protocol. If you are interested in a custom protocol that uses the thermocycler to your lab's specific needs, you can request one from our Applications Engineering Team, using the Protocol Request Form.\nWith this protocol, you can specify the traditional thermocycler parameters (denaturation temperature/time, annealation temperature/time, elongation temperature/time).\nAdditionally, you can specify the lid temperature, sample volume per well, an initialization temperature/time, a final elongation temperature/time, and a final hold temperature that will stay set until you're ready to move the samples.\nFor more information about the Opentrons Thermocycler Module, please see the Thermocycler Module white paper or our Thermocycler Module support article.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Thermocycler Module\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThe Thermocycler Module should be loaded into its default position in slots 7 and 10 (with some overhang in slots 8 and 11).\nBefore running the protocol with samples, use the button on top of the Thermocycler to open the lid (if closed) and place your sample plate into the Thermocycler. If needed, place an Opentrons Thermocycler Seal on the lid. You do not need to close the lid before running the protocol.\nUsing the customizations fields, below set up your thermocycler protocol.\n* Sample Volume per Well: Specify how much volume will be in each well for greater accuracy\n* Lid Temperature: Specify temperature of lid. We recommend a higher temperature to prevent condensation.\nInitialization\n* Initialization Temperature: Specify the temperature during the initialization phase (will not be cycled)\n* Initializatin Time: Specify the time during the initialization phase (will not be cycled)\nThermocycling\n* Denaturation Temperature: Specify the temperature during the denaturation phase (will be cycled)\n* Denaturation Time: Specify the time during the denaturation phase (will be cycled)\n* Annealation Temperature: Specify the temperature during the annealation phase (will be cycled)\n* Annealation Time: Specify the time during the annealtion phase (will be cycled)\n* Elongation Temperature: Specify the temperature during the elongation phase (will be cycled)\n* Elongation Time: Specify the time during the elongation phase (will be cycled)\n* Number of Cycles: Specify how many cycles to run the Denaturation-Annealation-Elongation loop\nFinal Elongation and Hold\n* Final Elongation Temperature: Specify the temperature during the final elongation phase (will not be cycled)\n* Final Elongation Time: Specify the time during the final elongation phase (will not be cycled)\n* Final Hold Temperature: Specify the final temperature the thermocycler will hold indefinitely.", + "description": "This is a demo protocol, intended for using the Opentrons Thermocycler Module as a thermocycler. This protocol does not involve any liquid handling, so no pipettes are required to run this protocol. If you are interested in a custom protocol that uses the thermocycler to your lab's specific needs, you can request one from our Applications Engineering Team, using the Protocol Request Form.\nWith this protocol, you can specify the traditional thermocycler parameters (denaturation temperature/time, annealation temperature/time, elongation temperature/time).\nAdditionally, you can specify the lid temperature, sample volume per well, an initialization temperature/time, a final elongation temperature/time, and a final hold temperature that will stay set until you're ready to move the samples.\nFor more information about the Opentrons Thermocycler Module, please see the Thermocycler Module white paper or our Thermocycler Module support article.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.15.0 or later)\nOpentrons Thermocycler Module\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nThe Thermocycler Module should be loaded into its default position in slots 7 and 10 (with some overhang in slots 8 and 11).\nBefore running the protocol with samples, use the button on top of the Thermocycler to open the lid (if closed) and place your sample plate into the Thermocycler. If needed, place an Opentrons Thermocycler Seal on the lid. You do not need to close the lid before running the protocol.\nUsing the customizations fields, below set up your thermocycler protocol.\n Sample Volume per Well: Specify how much volume will be in each well for greater accuracy\n Lid Temperature: Specify temperature of lid. We recommend a higher temperature to prevent condensation.\nInitialization\n Initialization Temperature: Specify the temperature during the initialization phase (will not be cycled)\n Initializatin Time: Specify the time during the initialization phase (will not be cycled)\nThermocycling\n Denaturation Temperature: Specify the temperature during the denaturation phase (will be cycled)\n Denaturation Time: Specify the time during the denaturation phase (will be cycled)\n Annealation Temperature: Specify the temperature during the annealation phase (will be cycled)\n Annealation Time: Specify the time during the annealtion phase (will be cycled)\n Elongation Temperature: Specify the temperature during the elongation phase (will be cycled)\n Elongation Time: Specify the time during the elongation phase (will be cycled)\n* Number of Cycles: Specify how many cycles to run the Denaturation-Annealation-Elongation loop\nFinal Elongation and Hold\n Final Elongation Temperature: Specify the temperature during the final elongation phase (will not be cycled)\n Final Elongation Time: Specify the time during the final elongation phase (will not be cycled)\n* Final Hold Temperature: Specify the final temperature the thermocycler will hold indefinitely.", "internal": "thermocycler", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-quick-custom/README.json b/protoBuilds/zymo-quick-custom/README.json index fc69612ef..9777c8ac9 100644 --- a/protoBuilds/zymo-quick-custom/README.json +++ b/protoBuilds/zymo-quick-custom/README.json @@ -5,7 +5,7 @@ "Zymo Kit" ] }, - "description": "This protocol automates nucleic acid purification with the Zymo Quick-DNA/RNA Viral MagBead Kit. This protocol is a continuation of the original Zymo Quick Extraction protocol which can be found in our Protocol Library here. More specifically, this protocol distributes PCR mastermix to the plate before the elute is distributed. \n\nUsing the P300 Multi-Channel Pipette and a Single-Channel Pipette, this protocol can accommodate up to 48 samples per run and can be configured to run any multiple of 8 up to 48. Starting with 400\u00b5L of sample in a deepwell plate, the entire process is automated and ends with 60\u00b5L of elution containing nucleic acid dispensed into a 96-well PCR plate.The elution is then ready for RT/qPCR, Next-Gen Sequencing, hybridization, etc.\n\nThis kit can be used for Station B (RNA extraction) of our COVID Workstation.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module, GEN2\nOpentrons P300 Multi-Channel Pipette\n(5) Opentrons 200\u00b5L Filter Tips (recommended) or Opentrons 300\u00b5L Tips\nOpentrons P20 (or P10) Single-Channel Pipette\nOpentrons 20\u00b5L Filter Tips\nNEST 96-Deep Well Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir\nNEST 1-Well Reservoir\nOpentrons 4-in-1 Tube Rack\n1.5mL Centrifuge Tube\nZymo Quick-DNA/RNA Viral MagBead Kit\nSamples\n15mL Falcon Tube\n\n\n\nReagent Preparation\nPrepare all reagents according to Zymo manual.\n\n\n\n\nProteinase K: In 1.5mL centrifuge tube, placed in \"D1\" in Opentrons 4-in-1 Tube Rack with 24-slot top.\nViral DNA/RNA Buffer + MagBinding Beads: In slots 1, 2, and 3 in the 12-well reservoir. For every column (8 samples), 7mL of Viral DNA/RNA Buffer should be combined with 175\u00b5L of MagBinding Beads. Up to two columns (16 samples) worth of buffer+beads can be prepared in one Falcon Tube at a time. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 1 would get 14mL buffer + 350\u00b5L beads, slot 2 would get 7mL buffer + 175\u00b5L beads, slot 3 would be empty).\nMagBead DNA/RNA Wash 1: In slots 4 and 5 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 4 would get 13.5mL, slot 5 would be empty).\nMagBead DNA/RNA Wash 2: In slots 6 and 7 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 6 would get 13.5mL, slot 7 would be empty).\nEthanol Wash 1: In slots 8 and 9 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 8 would get 13.5mL, slot 9 would be empty).\nEthanol Wash 2: In slots 10 and 11 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 10 would get 13.5mL, slot 11 would be empty).\nNuclease-Free Water: In slot 12 in the 12-well reservoir. To accommodate 24 samples or less, 4mL of water should be used. For more than 24 samples, 4.5-5mL of water can be used.\nPCR Mastermix: In tube D6 of the tube rack.\n\nDeck Layout\n\n\nSlot 1:: Opentrons 200\u00b5L Filter Tips\nSlot 2:: NEST 12-Well Reservoir with Zymo Kit Reagents\nSlot 3:: NEST 96-Well PCR Plate\nSlot 4:: Opentrons Magnetic Module with NEST 96-Deep Well Plate, 2mL loaded with 400\u00b5L of sample in odd columns\nSlot 5:: Opentrons 10/20\u00b5L Filter Tips\nSlot 6:: Opentrons 200\u00b5L Filter Tips\nSlot 7:: Opentrons 200\u00b5L Filter Tips\nSlot 8:: Opentrons 4-in-1 Tube Rack with Proteinase K in \"D1\"\nSlot 9:: Opentrons 200\u00b5L Filter Tips\nSlot 10:: Opentrons 200\u00b5L Filter Tips\nSlot 11:: NEST 1-Well Reservoir, empty for liquid waste\n\nNote about tips: Each column of samples (8) requires ten columns of tips for this extraction. For 48 samples, all the tips in the five tip racks will be used; if running less than 48 samples, less tips/tipracks will be used and the tipracks will be accessed in this slot order: 1, 6, 9, 7, 10.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Select the number of samples to run\n* P300-Multi Generation: Select which mount to place the P300 Gen2 Multi Channel Pipette\n* Single Channel Pipette: Select which mount to place the P20 Gen2 Single Channel Pipette", + "description": "This protocol automates nucleic acid purification with the Zymo Quick-DNA/RNA Viral MagBead Kit. This protocol is a continuation of the original Zymo Quick Extraction protocol which can be found in our Protocol Library here. More specifically, this protocol distributes PCR mastermix to the plate before the elute is distributed. \n\nUsing the P300 Multi-Channel Pipette and a Single-Channel Pipette, this protocol can accommodate up to 48 samples per run and can be configured to run any multiple of 8 up to 48. Starting with 400\u00b5L of sample in a deepwell plate, the entire process is automated and ends with 60\u00b5L of elution containing nucleic acid dispensed into a 96-well PCR plate.The elution is then ready for RT/qPCR, Next-Gen Sequencing, hybridization, etc.\n\nThis kit can be used for Station B (RNA extraction) of our COVID Workstation.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module, GEN2\nOpentrons P300 Multi-Channel Pipette\n(5) Opentrons 200\u00b5L Filter Tips (recommended) or Opentrons 300\u00b5L Tips\nOpentrons P20 (or P10) Single-Channel Pipette\nOpentrons 20\u00b5L Filter Tips\nNEST 96-Deep Well Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir\nNEST 1-Well Reservoir\nOpentrons 4-in-1 Tube Rack\n1.5mL Centrifuge Tube\nZymo Quick-DNA/RNA Viral MagBead Kit\nSamples\n15mL Falcon Tube\n\n\n\nReagent Preparation\nPrepare all reagents according to Zymo manual.\n\n\n\n\nProteinase K: In 1.5mL centrifuge tube, placed in \"D1\" in Opentrons 4-in-1 Tube Rack with 24-slot top.\nViral DNA/RNA Buffer + MagBinding Beads: In slots 1, 2, and 3 in the 12-well reservoir. For every column (8 samples), 7mL of Viral DNA/RNA Buffer should be combined with 175\u00b5L of MagBinding Beads. Up to two columns (16 samples) worth of buffer+beads can be prepared in one Falcon Tube at a time. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 1 would get 14mL buffer + 350\u00b5L beads, slot 2 would get 7mL buffer + 175\u00b5L beads, slot 3 would be empty).\nMagBead DNA/RNA Wash 1: In slots 4 and 5 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 4 would get 13.5mL, slot 5 would be empty).\nMagBead DNA/RNA Wash 2: In slots 6 and 7 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 6 would get 13.5mL, slot 7 would be empty).\nEthanol Wash 1: In slots 8 and 9 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 8 would get 13.5mL, slot 9 would be empty).\nEthanol Wash 2: In slots 10 and 11 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 10 would get 13.5mL, slot 11 would be empty).\nNuclease-Free Water: In slot 12 in the 12-well reservoir. To accommodate 24 samples or less, 4mL of water should be used. For more than 24 samples, 4.5-5mL of water can be used.\nPCR Mastermix: In tube D6 of the tube rack.\n\nDeck Layout\n\n\nSlot 1:: Opentrons 200\u00b5L Filter Tips\nSlot 2:: NEST 12-Well Reservoir with Zymo Kit Reagents\nSlot 3:: NEST 96-Well PCR Plate\nSlot 4:: Opentrons Magnetic Module with NEST 96-Deep Well Plate, 2mL loaded with 400\u00b5L of sample in odd columns\nSlot 5:: Opentrons 10/20\u00b5L Filter Tips\nSlot 6:: Opentrons 200\u00b5L Filter Tips\nSlot 7:: Opentrons 200\u00b5L Filter Tips\nSlot 8:: Opentrons 4-in-1 Tube Rack with Proteinase K in \"D1\"\nSlot 9:: Opentrons 200\u00b5L Filter Tips\nSlot 10:: Opentrons 200\u00b5L Filter Tips\nSlot 11:: NEST 1-Well Reservoir, empty for liquid waste\n\nNote about tips: Each column of samples (8) requires ten columns of tips for this extraction. For 48 samples, all the tips in the five tip racks will be used; if running less than 48 samples, less tips/tipracks will be used and the tipracks will be accessed in this slot order: 1, 6, 9, 7, 10.\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Select the number of samples to run\n P300-Multi Generation: Select which mount to place the P300 Gen2 Multi Channel Pipette\n* Single Channel Pipette: Select which mount to place the P20 Gen2 Single Channel Pipette", "internal": "zymo-quick-pcr", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-quick/README.json b/protoBuilds/zymo-quick/README.json index 417c044cb..c6b2692b8 100644 --- a/protoBuilds/zymo-quick/README.json +++ b/protoBuilds/zymo-quick/README.json @@ -5,7 +5,7 @@ "Zymo Kit" ] }, - "description": "This protocol automates nucleic acid purification with the Zymo Quick-DNA/RNA Viral MagBead Kit.\n\nUsing the P300 Multi-Channel Pipette and a Single-Channel Pipette, this protocol can accommodate up to 48 samples per run and can be configured to run any multiple of 8 up to 48. Starting with 400\u00b5L of sample in a deepwell plate, the entire process is automated and ends with 60\u00b5L of elution containing nucleic acid dispensed into a 96-well PCR plate. The elution is then ready for RT/qPCR, Next-Gen Sequencing, hybridization, etc.\n\nThis kit can be used for Station B (RNA extraction) of our COVID Workstation.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module, GEN1\nOpentrons P300 Multi-Channel Pipette\n(5) Opentrons 200\u00b5L Filter Tips (recommended) or Opentrons 300\u00b5L Tips\nOpentrons P20 (or P10) Single-Channel Pipette\nOpentrons 10/20\u00b5L Filter Tips\nNEST 96-Deep Well Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir\nNEST 1-Well Reservoir\nOpentrons 4-in-1 Tube Rack\n1.5mL Centrifuge Tube\nZymo Quick-DNA/RNA Viral MagBead Kit\nSamples\n15mL Falcon Tube\n\n\n\nReagent Preparation\nPrepare all reagents according to Zymo manual.\n\n\n\n\nProteinase K: In 1.5mL centrifuge tube, placed in \"D1\" in Opentrons 4-in-1 Tube Rack with 24-slot top.\nViral DNA/RNA Buffer + MagBinding Beads: In slots 1, 2, and 3 in the 12-well reservoir. For every column (8 samples), 7mL of Viral DNA/RNA Buffer should be combined with 175\u00b5L of MagBinding Beads. Up to two columns (16 samples) worth of buffer+beads can be prepared in one Falcon Tube at a time. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 1 would get 14mL buffer + 350\u00b5L beads, slot 2 would get 7mL buffer + 175\u00b5L beads, slot 3 would be empty).\nMagBead DNA/RNA Wash 1: In slots 4 and 5 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 4 would get 13.5mL, slot 5 would be empty).\nMagBead DNA/RNA Wash 2: In slots 6 and 7 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 6 would get 13.5mL, slot 7 would be empty).\nEthanol Wash 1: In slots 8 and 9 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 8 would get 13.5mL, slot 9 would be empty).\nEthanol Wash 2: In slots 10 and 11 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 10 would get 13.5mL, slot 11 would be empty).\nNuclease-Free Water: In slot 12 in the 12-well reservoir. To accommodate 24 samples or less, 4mL of water should be used. For more than 24 samples, 4.5-5mL of water can be used.\n\nDeck Layout\n\n\nSlot 1:: Opentrons 200\u00b5L Filter Tips\nSlot 2:: NEST 12-Well Reservoir with Zymo Kit Reagents\nSlot 3:: NEST 96-Well PCR Plate\nSlot 4:: Opentrons Magnetic Module with NEST 96-Deep Well Plate, 2mL loaded with 400\u00b5L of sample in odd columns\nSlot 5:: Opentrons 10/20\u00b5L Filter Tips\nSlot 6:: Opentrons 200\u00b5L Filter Tips\nSlot 7:: Opentrons 200\u00b5L Filter Tips\nSlot 8:: Opentrons 4-in-1 Tube Rack with Proteinase K in \"D1\"\nSlot 9:: Opentrons 200\u00b5L Filter Tips\nSlot 10:: Opentrons 200\u00b5L Filter Tips\nSlot 11:: NEST 1-Well Reservoir, empty for liquid waste\n\nNote about tips: Each column of samples (8) requires ten columns of tips for this extraction. For 48 samples, all the tips in the five tip racks will be used; if running less than 48 samples, less tips/tipracks will be used and the tipracks will be accessed in this slot order: 1, 6, 9, 7, 10.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Samples: Select the number of samples to run\n* P300-Multi Generation: Select which generation P300-Multi is being used\n* Single Channel Pipette: Select which single channel pipette is being used", + "description": "This protocol automates nucleic acid purification with the Zymo Quick-DNA/RNA Viral MagBead Kit.\n\nUsing the P300 Multi-Channel Pipette and a Single-Channel Pipette, this protocol can accommodate up to 48 samples per run and can be configured to run any multiple of 8 up to 48. Starting with 400\u00b5L of sample in a deepwell plate, the entire process is automated and ends with 60\u00b5L of elution containing nucleic acid dispensed into a 96-well PCR plate. The elution is then ready for RT/qPCR, Next-Gen Sequencing, hybridization, etc.\n\nThis kit can be used for Station B (RNA extraction) of our COVID Workstation.\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons Magnetic Module, GEN1\nOpentrons P300 Multi-Channel Pipette\n(5) Opentrons 200\u00b5L Filter Tips (recommended) or Opentrons 300\u00b5L Tips\nOpentrons P20 (or P10) Single-Channel Pipette\nOpentrons 10/20\u00b5L Filter Tips\nNEST 96-Deep Well Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir\nNEST 1-Well Reservoir\nOpentrons 4-in-1 Tube Rack\n1.5mL Centrifuge Tube\nZymo Quick-DNA/RNA Viral MagBead Kit\nSamples\n15mL Falcon Tube\n\n\n\nReagent Preparation\nPrepare all reagents according to Zymo manual.\n\n\n\n\nProteinase K: In 1.5mL centrifuge tube, placed in \"D1\" in Opentrons 4-in-1 Tube Rack with 24-slot top.\nViral DNA/RNA Buffer + MagBinding Beads: In slots 1, 2, and 3 in the 12-well reservoir. For every column (8 samples), 7mL of Viral DNA/RNA Buffer should be combined with 175\u00b5L of MagBinding Beads. Up to two columns (16 samples) worth of buffer+beads can be prepared in one Falcon Tube at a time. Each slot of the 12 well reservoir can accommodate volume for 2 columns/16 samples and should be loaded sequentially (ex. if running 24 samples, slot 1 would get 14mL buffer + 350\u00b5L beads, slot 2 would get 7mL buffer + 175\u00b5L beads, slot 3 would be empty).\nMagBead DNA/RNA Wash 1: In slots 4 and 5 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 4 would get 13.5mL, slot 5 would be empty).\nMagBead DNA/RNA Wash 2: In slots 6 and 7 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 6 would get 13.5mL, slot 7 would be empty).\nEthanol Wash 1: In slots 8 and 9 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 8 would get 13.5mL, slot 9 would be empty).\nEthanol Wash 2: In slots 10 and 11 in the 12-well reservoir. Each slot can accommodate enough volume for 24 samples (3 columns). Each slot would get 13.5mL if running 48 samples and would be scaled back if running less (ex. if running 24 samples, slot 10 would get 13.5mL, slot 11 would be empty).\nNuclease-Free Water: In slot 12 in the 12-well reservoir. To accommodate 24 samples or less, 4mL of water should be used. For more than 24 samples, 4.5-5mL of water can be used.\n\nDeck Layout\n\n\nSlot 1:: Opentrons 200\u00b5L Filter Tips\nSlot 2:: NEST 12-Well Reservoir with Zymo Kit Reagents\nSlot 3:: NEST 96-Well PCR Plate\nSlot 4:: Opentrons Magnetic Module with NEST 96-Deep Well Plate, 2mL loaded with 400\u00b5L of sample in odd columns\nSlot 5:: Opentrons 10/20\u00b5L Filter Tips\nSlot 6:: Opentrons 200\u00b5L Filter Tips\nSlot 7:: Opentrons 200\u00b5L Filter Tips\nSlot 8:: Opentrons 4-in-1 Tube Rack with Proteinase K in \"D1\"\nSlot 9:: Opentrons 200\u00b5L Filter Tips\nSlot 10:: Opentrons 200\u00b5L Filter Tips\nSlot 11:: NEST 1-Well Reservoir, empty for liquid waste\n\nNote about tips: Each column of samples (8) requires ten columns of tips for this extraction. For 48 samples, all the tips in the five tip racks will be used; if running less than 48 samples, less tips/tipracks will be used and the tipracks will be accessed in this slot order: 1, 6, 9, 7, 10.\n\nUsing the customizations field (below), set up your protocol.\n Number of Samples: Select the number of samples to run\n P300-Multi Generation: Select which generation P300-Multi is being used\n* Single Channel Pipette: Select which single channel pipette is being used", "internal": "zymo-quick", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-ribofree-cleanup/README.json b/protoBuilds/zymo-ribofree-cleanup/README.json index ae23815eb..9d6c13b19 100644 --- a/protoBuilds/zymo-ribofree-cleanup/README.json +++ b/protoBuilds/zymo-ribofree-cleanup/README.json @@ -5,7 +5,7 @@ "Zymo RiboFree\u2122 Total RNA Library Prep" ] }, - "description": "This protocol performs Select-a-Size MagBead Clean-up for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on a second OT-2 in conjunction with another OT-2 running the rest of the library prep (first strand cDNA synthesis, universal depletion, P7 and P5 adapter ligations, and library index PCR).\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n* First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n* P7 Adapter Ligation (robot 1)\n* P5 Adapter Ligation (robot 1)\n* Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Temperature Module GEN2\nOpentrons Magnetic Module GEN2 for NEST 96-well PCR plate, full skirt\nNEST 12-channel reservoir 15ml\nOpentrons P20 and P300 GEN2 multi-channel pipettes\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\n12-channel reservoir (slot 2)\n", + "description": "This protocol performs Select-a-Size MagBead Clean-up for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on a second OT-2 in conjunction with another OT-2 running the rest of the library prep (first strand cDNA synthesis, universal depletion, P7 and P5 adapter ligations, and library index PCR).\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n P7 Adapter Ligation (robot 1)\n P5 Adapter Ligation (robot 1)\n Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Temperature Module GEN2\nOpentrons Magnetic Module GEN2 for NEST 96-well PCR plate, full skirt\nNEST 12-channel reservoir 15ml\nOpentrons P20 and P300 GEN2 multi-channel pipettes\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\n12-channel reservoir (slot 2)\n", "internal": "zymo-ribofree", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/README.json b/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/README.json index 07aeda072..e6a362f94 100644 --- a/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/README.json +++ b/protoBuilds/zymo-ribofree-first-strand-cdna-synth-universal-depletion/README.json @@ -5,7 +5,7 @@ "Zymo RiboFree\u2122 Total RNA Library Prep" ] }, - "description": "This protocol performs First-Strand cDNA Synthesis and RiboFreeTM Universal Depletion for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n* First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n* P7 Adapter Ligation (robot 1)\n* P5 Adapter Ligation (robot 1)\n* Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons P20 GEN2 multi-channel pipette\nOpentrons 20\u00b5l tipracks\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", + "description": "This protocol performs First-Strand cDNA Synthesis and RiboFreeTM Universal Depletion for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n P7 Adapter Ligation (robot 1)\n P5 Adapter Ligation (robot 1)\n Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons P20 GEN2 multi-channel pipette\nOpentrons 20\u00b5l tipracks\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", "internal": "zymo-ribofree", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-ribofree-library-index-pcr/README.json b/protoBuilds/zymo-ribofree-library-index-pcr/README.json index 827d82920..c559b254b 100644 --- a/protoBuilds/zymo-ribofree-library-index-pcr/README.json +++ b/protoBuilds/zymo-ribofree-library-index-pcr/README.json @@ -5,7 +5,7 @@ "Zymo RiboFree\u2122 Total RNA Library Prep" ] }, - "description": "This protocol performs Library Index PCR for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Indexes on the UDI Primer plate will be transferred to the corresponding well of the sample plate on the thermocycler module. Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nLinks:\n* First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n* P7 Adapter Ligation (robot 1)\n* P5 Adapter Ligation (robot 1)\n* Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons P50 GEN1 multi-channel pipette\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", + "description": "This protocol performs Library Index PCR for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Indexes on the UDI Primer plate will be transferred to the corresponding well of the sample plate on the thermocycler module. Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nLinks:\n First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n P7 Adapter Ligation (robot 1)\n P5 Adapter Ligation (robot 1)\n Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons P50 GEN1 multi-channel pipette\nOpentrons 20\u00b5l and 50/300\u00b5l tipracks\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", "internal": "zymo-ribofree", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-ribofree-p5-adapter-ligation/README.json b/protoBuilds/zymo-ribofree-p5-adapter-ligation/README.json index e202f83fe..31cecdf9e 100644 --- a/protoBuilds/zymo-ribofree-p5-adapter-ligation/README.json +++ b/protoBuilds/zymo-ribofree-p5-adapter-ligation/README.json @@ -5,7 +5,7 @@ "Zymo RiboFree\u2122 Total RNA Library Prep" ] }, - "description": "This protocol performs P5 Adapter Ligation for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n* First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n* P7 Adapter Ligation (robot 1)\n* P5 Adapter Ligation (robot 1)\n* Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons P20 GEN2 multi-channel pipette\nOpentrons 20\u00b5l tipracks\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", + "description": "This protocol performs P5 Adapter Ligation for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n P7 Adapter Ligation (robot 1)\n P5 Adapter Ligation (robot 1)\n Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons P20 GEN2 multi-channel pipette\nOpentrons 20\u00b5l tipracks\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", "internal": "zymo-ribofree", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-ribofree-p7-adapter-ligation/README.json b/protoBuilds/zymo-ribofree-p7-adapter-ligation/README.json index df1bccabf..c4f4e3886 100644 --- a/protoBuilds/zymo-ribofree-p7-adapter-ligation/README.json +++ b/protoBuilds/zymo-ribofree-p7-adapter-ligation/README.json @@ -5,7 +5,7 @@ "Zymo RiboFree\u2122 Total RNA Library Prep" ] }, - "description": "This protocol performs P7 Adapter Ligation for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n* First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n* P7 Adapter Ligation (robot 1)\n* P5 Adapter Ligation (robot 1)\n* Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons 20\u00b5l\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", + "description": "This protocol performs P7 Adapter Ligation for the Zymo-Seq RiboFree\u2122 Total RNA Library Prep. This protocol is meant to be run on one OT-2 in conjunction with a second OT-2 running solely Select-a-Size MagBead Clean-up Protocol.\nSamples will be processed down columns and then across rows (A1, B1, C1, ... A2, B2, etc.). Thoroughly mix reagent tubes thoroughly by flicking or pipetting before starting. Briefly spin down and load onto the temperature module according to Setup below.\nThe user is prompted to replace tipracks mid-protocol when necessary (for > 76 samples).\nLinks:\n First Strand cDNA Synthesis and RiboFreeTM Universal Depletion (robot 1)\n P7 Adapter Ligation (robot 1)\n P5 Adapter Ligation (robot 1)\n Library Index PCR (robot 1)\n* Select-a-Size Magbead Clean-up (robot 2)\n\n\n\nOpentrons Thermocycler Module with NEST 96-well PCR plate, full skirt\nOpentrons Temperature Module GEN2 with 4x6 aluminum block for NEST 1.5ml screwcap reagent tubes\nNEST 12-channel reservoir 15ml\nOpentrons P20 GEN2 single-channel pipette\nOpentrons 20\u00b5l\n\n\n\n4x6 aluminum block on temperature module (slot 1)\n\n12-channel reservoir (slot 2)\n", "internal": "zymo-ribofree", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", diff --git a/protoBuilds/zymo-rna-extraction/README.json b/protoBuilds/zymo-rna-extraction/README.json index ba6a9556a..041c10137 100644 --- a/protoBuilds/zymo-rna-extraction/README.json +++ b/protoBuilds/zymo-rna-extraction/README.json @@ -5,7 +5,7 @@ "RNA Extraction" ] }, - "description": "This protocol automates the Zymo Quick-DNA/RNA Viral MagBead Extraction Kit. This kit is designed for high-throughput purification of viral DNA and/or RNA and the isolated nucleic acids are ready for all downstream applications, such as RT-qPCR, Next-Gen Sequencing, and many others.\n\nThis kit can be used for Station B (RNA extraction) as part of our COVID Workstation.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.16.0 or later)\nOpentrons Magnetic Module\nOpentrons Temperature Module with 96-Well Aluminum Block\nOpentrons P20 Single-Channel Pipette\nOpentrons P300 8-Channel Pipette, Gen 2\nOpentrons 200\u00b5L Filter Tips\nOpentrons 20\u00b5L Filter Tips\nOpentrons 4-in-1 Tube Rack with 24-Well Top\nNEST 1.5mL Microcentrifuge Tubes\nNEST 96-Deepwell Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nZymo Quick-DNA/RNA Viral MagBead Kit\nEthanol, 95-100%\nSample, 400\u00b5L per well\n\n\n\nNote - Before running this protocol, make sure you clean the OT-2. For more information on cleaning the OT-2, check out this guide.\n\nThe setup for this protocol varies slightly, depending on the number of samples the user selects.\n\nLabware Setup\n\nSlot 2: NEST 12-Well Reservoir, 15mL with reagents (see below)\n\nSlot 3: Opentrons Temperature Module with 96-Well Aluminum Block with clean and empty NEST 96-Well PCR Plate\n\nSlot 4: Opentrons Magnetic Module with NEST 96-Deepwell Plate, 2mL, containing samples\nSamples should be loaded in odd-numbered columns only*\n\nSlot 5: Opentrons 20\u00b5L Filter Tips\n\nSlot 8: Opentrons 4-in-1 Tube Rack with 24-Well Top, containing reagents in NEST 1.5mL Microcentrifuge Tubes (see below)\n\nOpentrons 200\u00b5L Filter Tips\n* if 8 samples, Slot 1\n* if 16 samples, Slots 1 and 6\n* if 24 samples, Slots 1, 6, and 9\n* if 32 samples, Slots 1, 6, 7, and 9\n* if 40 or 48 samples, Slots 1, 6, 7, 9, and 10\n\n\nReagent Setup\n\nOpentrons 4-in-1 Tube Rack with 24-Well Top\nD1: Proteinase K, 4\u00b5L per sample\nD6: Extraction Control Spike-In, if using\n\nNEST 12-Well Reservoir, 15mL\nFor every 8 samples, the following reagents are needed:\n* 7mL Zymo Viral DNA/RNA Buffer + 350\u00b5L of Zymo MagBeads\n* 4.5mL of Zymo Wash Buffer 1\n* 4.5mL of Zymo Wash Buffer 2\n* 4.5mL of Ethanol (Ethanol Wash 1)\n* 4.5mL Ethanol (Ethanol Wash 2)\n\nSlot 1: Zymo Viral DNA/RNA Buffer + Zymo MagBeads, 8/16 samples\nSlot 2: Zymo Viral DNA/RNA Buffer + Zymo MagBeads, 24/32 samples\nSlot 3: Zymo Viral DNA/RNA Buffer + Zymo MagBeads, 40/48 samples\nSlot 4: Zymo Wash Buffer 1, 8/16/24 samples\nSlot 5: Zymo Wash Buffer 1, 32/40/48 samples\nSlot 6: Zymo Wash Buffer 2, 8/16/24 samples\nSlot 7: Zymo Wash Buffer 2, 32/40/48 samples\nSlot 8: Ethanol (Ethanol Wash 1), 8/16/24 samples\nSlot 9: Ethanol (Ethanol Wash 1), 32/40/48 samples\nSlot 10: Ethanol (Ethanol Wash 2), 8/16/24 samples\nSlot 11: Ethanol (Ethanol Wash 2), 32/40/48 samples\nSlot 12: Nuclease-Free Water, 3.5-4mL\n\nFull Deck Layout:\n\nUsing the customizations fields, below set up your protocol.\n* Number of Samples: Specify the number of samples you'd like to run.\n* Amount of Spike-in: Specify how much control RNA (or other spike-in) should be added to each well. If not using a spike-in, leave as 0.\n* Return tips after wash step: Specify whether to drop tips into trash bin after use, or to replace in tip rack for easy disposal.", + "description": "This protocol automates the Zymo Quick-DNA/RNA Viral MagBead Extraction Kit. This kit is designed for high-throughput purification of viral DNA and/or RNA and the isolated nucleic acids are ready for all downstream applications, such as RT-qPCR, Next-Gen Sequencing, and many others.\n\nThis kit can be used for Station B (RNA extraction) as part of our COVID Workstation.\n\n\nTo purchase consumables, labware, or pipettes, please visit our online store or contact our sales team at info@opentrons.com\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.16.0 or later)\nOpentrons Magnetic Module\nOpentrons Temperature Module with 96-Well Aluminum Block\nOpentrons P20 Single-Channel Pipette\nOpentrons P300 8-Channel Pipette, Gen 2\nOpentrons 200\u00b5L Filter Tips\nOpentrons 20\u00b5L Filter Tips\nOpentrons 4-in-1 Tube Rack with 24-Well Top\nNEST 1.5mL Microcentrifuge Tubes\nNEST 96-Deepwell Plate, 2mL\nNEST 96-Well PCR Plate\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nZymo Quick-DNA/RNA Viral MagBead Kit\nEthanol, 95-100%\nSample, 400\u00b5L per well\n\n\n\nNote - Before running this protocol, make sure you clean the OT-2. For more information on cleaning the OT-2, check out this guide.\n\nThe setup for this protocol varies slightly, depending on the number of samples the user selects.\n\nLabware Setup\n\nSlot 2: NEST 12-Well Reservoir, 15mL with reagents (see below)\n\nSlot 3: Opentrons Temperature Module with 96-Well Aluminum Block with clean and empty NEST 96-Well PCR Plate\n\nSlot 4: Opentrons Magnetic Module with NEST 96-Deepwell Plate, 2mL, containing samples\nSamples should be loaded in odd-numbered columns only\n\nSlot 5: Opentrons 20\u00b5L Filter Tips\n\nSlot 8: Opentrons 4-in-1 Tube Rack with 24-Well Top, containing reagents in NEST 1.5mL Microcentrifuge Tubes (see below)\n\nOpentrons 200\u00b5L Filter Tips\n if 8 samples, Slot 1\n if 16 samples, Slots 1 and 6\n if 24 samples, Slots 1, 6, and 9\n if 32 samples, Slots 1, 6, 7, and 9\n if 40 or 48 samples, Slots 1, 6, 7, 9, and 10\n\n\nReagent Setup\n\nOpentrons 4-in-1 Tube Rack with 24-Well Top\nD1: Proteinase K, 4\u00b5L per sample\nD6: Extraction Control Spike-In, if using\n\nNEST 12-Well Reservoir, 15mL\nFor every 8 samples, the following reagents are needed:\n 7mL Zymo Viral DNA/RNA Buffer + 350\u00b5L of Zymo MagBeads\n 4.5mL of Zymo Wash Buffer 1\n 4.5mL of Zymo Wash Buffer 2\n 4.5mL of Ethanol (Ethanol Wash 1)\n* 4.5mL Ethanol (Ethanol Wash 2)\n\nSlot 1: Zymo Viral DNA/RNA Buffer + Zymo MagBeads, 8/16 samples\nSlot 2: Zymo Viral DNA/RNA Buffer + Zymo MagBeads, 24/32 samples\nSlot 3: Zymo Viral DNA/RNA Buffer + Zymo MagBeads, 40/48 samples\nSlot 4: Zymo Wash Buffer 1, 8/16/24 samples\nSlot 5: Zymo Wash Buffer 1, 32/40/48 samples\nSlot 6: Zymo Wash Buffer 2, 8/16/24 samples\nSlot 7: Zymo Wash Buffer 2, 32/40/48 samples\nSlot 8: Ethanol (Ethanol Wash 1), 8/16/24 samples\nSlot 9: Ethanol (Ethanol Wash 1), 32/40/48 samples\nSlot 10: Ethanol (Ethanol Wash 2), 8/16/24 samples\nSlot 11: Ethanol (Ethanol Wash 2), 32/40/48 samples\nSlot 12: Nuclease-Free Water, 3.5-4mL\n\nFull Deck Layout:\n\nUsing the customizations fields, below set up your protocol.\n Number of Samples: Specify the number of samples you'd like to run.\n Amount of Spike-in: Specify how much control RNA (or other spike-in) should be added to each well. If not using a spike-in, leave as 0.\n* Return tips after wash step: Specify whether to drop tips into trash bin after use, or to replace in tip rack for easy disposal.", "internal": "zymo-rna-extraction", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", From 1d4f34987c4ed0c5cda11e2bb1406d09ed221487 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E2=80=9Cramifarawi=E2=80=9D?= <“rami.farawi@opentrons.com”> Date: Fri, 8 Sep 2023 17:06:47 -0400 Subject: [PATCH 6/6] fix --- protoBuilds/0b97ae-protocol-3B/README.json | 4 ++-- protocols/0b97ae-protocol-3B/README.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/protoBuilds/0b97ae-protocol-3B/README.json b/protoBuilds/0b97ae-protocol-3B/README.json index ea26a58e6..58e81b6c9 100644 --- a/protoBuilds/0b97ae-protocol-3B/README.json +++ b/protoBuilds/0b97ae-protocol-3B/README.json @@ -12,7 +12,7 @@ "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* NGS LIBRARY PREP\n\t* QIASeq FastSelect\n\n\n", - "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/3F240714-EB34-4978-97F6-5BD0739E874B_1_105_c.jpeg)\nWater Reservoir (slot 2):\n\tColumn 1: Nuclease Free Water\n\tColumn 2: Binding Buffer\n\tColumn 3 & 4: Ethanol\n\tColumn 10, 11 & 12: Empty for Supernatent Removal\nDiluted RNA Plate (slot 7 Temperature Module):\n\tRNA Samples Starting Plate\nReagent Plate (Slot 10):\n\tColumn 1: MasterMix\n\tColumn 2: Magentic Beads\n\n", + "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/deck.jpg)\nWater Reservoir (slot 2):\n\tColumn 1: Nuclease Free Water\n\tColumn 2: Binding Buffer\n\tColumn 3 & 4: Ethanol\n\tColumn 10, 11 & 12: Empty for Supernatent Removal\nDiluted RNA Plate (slot 7 Temperature Module):\n\tRNA Samples Starting Plate\nReagent Plate (Slot 10):\n\tColumn 1: MasterMix\n\tColumn 2: Magentic Beads\n\n", "description": "This is Part 3 to the QIAseq FastSelect 5s, 16s, 23s Protocol. This protocol is used to perform the addition of samples with mastermix into a plate.\nPart 1 to this protocol is the normalization of samples.\nPart 2 to this protocol is the Fragementation.\n\nLinks:\n* [Part 1: Sample Normalization](http://protocols.opentrons.com/protocol/0b97ae)\n* [Part 2: QIAseq FastSelect 5s, 16s, 23s Fragmentation](http://protocols.opentrons.com/protocol/0b97ae-protocol-2B)\n* [Part 3: QIAseq FastSelect 5s, 16s, 23s Extraction](http://protocols.opentrons.com/protocol/0b97ae-protocol-3B)\n\n\n", "internal": "0b97ae-protocol-3B\n", "labware": "* Perkin Elmer 12 Reservoir 21000 \u00b5L\n* Applied Biosystems Enduraplate 96 Aluminum Block 220 \u00b5L\n* [Bio-Rad 96 Well Plate 200 \u00b5L PCR #hsp9601](http://www.bio-rad.com/en-us/sku/hsp9601-hard-shell-96-well-pcr-plates-low-profile-thin-wall-skirted-white-clear?ID=hsp9601)\n* Opentrons 96 Filter Tip Rack 20 \u00b5L\n* [NEST 96 Deepwell Plate 2mL #503001](http://www.cell-nest.com/page94?product_id=101&_l=en)\n* [Opentrons 96 Tip Rack 300 \u00b5L](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* [Opentrons 96 Well Aluminum Block with Bio-Rad Well Plate 200 \u00b5L](https://shop.opentrons.com/collections/hardware-modules/products/aluminum-block-set)\n\n\n", @@ -21,7 +21,7 @@ "pipettes": "* [Opentrons P20 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [Opentrons P300 8 Channel Electronic Pipette (GEN2)](https://shop.opentrons.com/8-channel-electronic-pipette/)\n\n\n", "process": "1. Input your protocol parameters above.\n2. Download your protocol and unzip if needed.\n3. Upload your custom labware to the [OT App](https://opentrons.com/ot-app) by navigating to `More` > `Custom Labware` > `Add Labware`, and selecting your labware files (.json extensions) if needed.\n4. Upload your protocol file (.py extension) to the [OT App](https://opentrons.com/ot-app) in the `Protocol` tab.\n5. Set up your deck according to the deck map.\n6. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support articles](https://support.opentrons.com/en/collections/1559720-guide-for-getting-started-with-the-ot-2).\n7. Hit \"Run\".\n\n\n", "protocol-steps": "1. Before this protocol the RNA plate should have went through the thermocycler according to FastSelect 5s/16s/23s, Table 3 and placed on a back on the temperature deck on slot 7.\n2. The Reagent plate will be placed on the temperature module on slot 10, which will contain MasterMix in column 1 and magentic beads in column 2.\n3. The reservoir will be placed on slot 2, which will contain Nucleas Free Water in well 1, Binding Buffer in well 2, and Ethanol in wells 3 and 4. Wells 10, 11 and 12 will be used for supernatent removal.\n\n\n\n", - "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/part+4/reagen.jpg)\n\n\n", + "reagent-setup": "![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/reagents.jpg)\n\n\n", "title": "QIAseq FastSelect Extraction" }, "modules": [ diff --git a/protocols/0b97ae-protocol-3B/README.md b/protocols/0b97ae-protocol-3B/README.md index 2e5a120a2..2fc3530ce 100644 --- a/protocols/0b97ae-protocol-3B/README.md +++ b/protocols/0b97ae-protocol-3B/README.md @@ -42,7 +42,7 @@ Links: ### Deck Setup -![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/3F240714-EB34-4978-97F6-5BD0739E874B_1_105_c.jpeg) +![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/deck.jpg) Water Reservoir (slot 2): Column 1: Nuclease Free Water Column 2: Binding Buffer @@ -55,7 +55,7 @@ Reagent Plate (Slot 10): Column 2: Magentic Beads ### Reagent Setup -![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/part+4/reagen.jpg) +![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/0b97ae/reagents.jpg) ### Protocol Steps