diff --git a/protoBuilds/274d2a/README.json b/protoBuilds/274d2a/README.json index a70d91ca5..81dfc8f85 100644 --- a/protoBuilds/274d2a/README.json +++ b/protoBuilds/274d2a/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Sample Prep": [ "Cherrypicking" @@ -8,7 +8,7 @@ "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# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/274d2a). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Sample Prep\n\t* Cherrypicking\n\n", "description": "![Cherrypicking Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/cherrypicking/cherrypicking_example.png)\n\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---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons Single-Channel Pipette](https://shop.opentrons.com/collections/ot-2-pipettes) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips)\n* [Microplates (96-well or 384-well)](https://labware.opentrons.com/?category=wellPlate)\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\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](https://shop.opentrons.com/collections/opentrons-tips), and the user will be prompted to refill the tipracks if all are emptied in the middle of the protocol.\n\n**CSV Format**\n\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!\n\nHere's an example of how a short cherrypicking protocol should be properly formatted:\n\n```\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\n```\n\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.\n\nIf you\u2019d like to follow our template, you can make a copy of [this spreadsheet](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/274d2a/ex.csv), fill out your values, and export as CSV for use with this protocol.\n\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.\n\n\n", "internal": "274d2a\n", diff --git a/protoBuilds/3359a5/README.json b/protoBuilds/3359a5/README.json index 1f0b06c0e..f8d98c018 100644 --- a/protoBuilds/3359a5/README.json +++ b/protoBuilds/3359a5/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Featured": [ "Cherrypicking" @@ -10,7 +10,7 @@ "internal": "3359a5", "labware": "\nAny verified labware found in our Labware Library\n", "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/3359a5). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Featured\n\t* Cherrypicking\n\n", "deck-setup": "Example Deck Setup - this is variable depending on the .csv uploaded.\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/3359a5/Screen+Shot+2021-04-29+at+2.45.06+PM.png)\n\n\n---\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.\n\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.\n\n\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](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/3359a5/template.csv) being sure to include the header line. Refer to our [Labware Library](https://labware.opentrons.com/?category=wellPlate) to copy API names for labware to include in the `source_labware` and `destination_labware` columns of the .csv.\n\n---\n\n", diff --git a/protoBuilds/6d901d-2/6d901d-2.ot2.apiv2.py.json b/protoBuilds/6d901d-2/6d901d-2.ot2.apiv2.py.json index e74a0f9f6..fd3b265be 100644 --- a/protoBuilds/6d901d-2/6d901d-2.ot2.apiv2.py.json +++ b/protoBuilds/6d901d-2/6d901d-2.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons import protocol_api\nfrom opentrons.protocol_api.labware import OutOfTipsError\n\n\nmetadata = {\n 'protocolName':\n ('Cherrypicking with multi-channel pipette substituting for a single '\n 'channel pipette'),\n 'author': 'Nick & Eskil ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.12'\n}\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n\n [transfer_csv,\n lw_source_plate,\n lw_source_plate_open,\n lw_dest_plate,\n lw_dest_plate_open,\n res_type,\n pipette_type,\n pipette_mount,\n tip_type,\n tip_reuse,\n starting_tiprack_slot,\n starting_tip_well] = get_values( # noqa: F821\n \"transfer_csv\",\n \"lw_source_plate\",\n \"lw_source_plate_open\",\n \"lw_dest_plate\",\n \"lw_dest_plate_open\",\n \"res_type\",\n \"pipette_type\",\n \"pipette_mount\",\n \"tip_type\",\n \"tip_reuse\",\n \"starting_tiprack_slot\",\n \"starting_tip_well\")\n\n tiprack_map = {\n 'p20_multi_gen2': {\n 'standard': 'opentrons_96_tiprack_20ul',\n 'filter': 'opentrons_96_filtertiprack_20ul'\n },\n 'p300_multi_gen2': {\n 'standard': 'opentrons_96_tiprack_300ul',\n 'filter': 'opentrons_96_filtertiprack_200ul'\n }\n }\n\n # Parse csv\n # Format: Source Well, Source Aspiration Height Above Bottom (in mm),\n # Dest Well, Volume (in ul)\n transfer_info = [[val.strip().lower() for val in line.split(',')]\n for line in transfer_csv.splitlines()\n if line.split(',')[0].strip()][1:]\n\n if lw_source_plate_open.strip():\n lw_source_plate_name = lw_source_plate_open\n else:\n lw_source_plate_name = lw_source_plate\n if lw_dest_plate_open.strip():\n lw_dest_plate_name = lw_dest_plate_open\n else:\n lw_dest_plate_name = lw_dest_plate\n\n # Load labware\n # Plate to cherrypick from\n source_plate = ctx.load_labware(lw_source_plate_name, '7')\n dest_plate = ctx.load_labware(lw_dest_plate_name, '8')\n # This reservoir is unused, but present\n if res_type != \"none\":\n ctx.load_labware(res_type, '9')\n\n # Load tipracks\n tip_name = tiprack_map[pipette_type][tip_type]\n tiprack_slots = ['4', '5', '10', '11']\n tipracks = [ctx.load_labware(tip_name, slot)\n for slot in tiprack_slots]\n\n # load pipette\n pip = ctx.load_instrument(pipette_type, pipette_mount, tip_racks=tipracks)\n\n if 'p20' in pipette_type:\n pick_up_current = 0.15\n ctx._hw_manager.hardware._attached_instruments[\n pip._implementation.get_mount()].update_config_item(\n 'pick_up_current', pick_up_current)\n\n # Tip_map has the columns reversed, pipette always picks up the\n # bottom-most tip in a given column until the column is depleted, and then\n # moves to the next column (from left to right).\n tip_map = []\n for rack in tipracks:\n tip_map.append(\n [[col for col in reversed(column)] for column in rack.columns()])\n # Flag at the end of each rack that is true if there are tips left\n for rack in tip_map:\n rack.append(True)\n # Flag used tipracks based on the protocol input parameter.\n # Check that the input parameter is an existing tiprack slot\n if starting_tiprack_slot not in tiprack_slots:\n raise Exception(\n f\"The Starting Tiprack Slot ({starting_tiprack_slot}) is invalid \"\n f\"The valid tiprack slots are {tiprack_slots}\"\n )\n start_rack_index = tiprack_slots.index(starting_tiprack_slot)\n for i in range(start_rack_index):\n tip_map[i][-1] = False\n\n # Flag used tips in the first available tiprack\n for column in tip_map[start_rack_index]:\n is_break = False\n for well in column:\n if well.well_name != starting_tip_well:\n well.has_tip = False\n else:\n is_break = True\n break\n if is_break:\n break\n\n def pick_up(pipette):\n \"\"\"`pick_up()` will pause the ctx when all tip boxes are out of\n tips, prompting the user to replace all tip racks. Once tipracks are\n reset, the ctx will start picking up tips from the first tip\n box as defined in the slot order when assigning the labware definition\n for that tip box. `pick_up()` will track tips for both pipettes if\n applicable.\n\n :param pipette: The pipette desired to pick up tip\n as definited earlier in the ctx (e.g. p300, m20).\n \"\"\"\n for i, rack in enumerate(tip_map):\n # Check the flag to see if the rack is empty, then we don't loop\n # through that rack so that the algorithm executes faster.\n if rack[-1] is False:\n if i == len(tip_map) - 1: # All tips are used, time to reset\n ctx.pause(\"Replace empty tip racks\")\n # print(\"Replace empty tip racks\")\n pipette.reset_tipracks()\n for rack in tip_map:\n rack[-1] = True\n # Raise an exception so that we can retry the pick up\n raise OutOfTipsError(\n \"Tipracks were out of tips and were reset\")\n else:\n continue\n for column in rack[:-1]: # skip [-1] index because it's the flag\n for well in column:\n if well.has_tip:\n pipette.pick_up_tip(well)\n if well.well_name == 'A12': # last tip in the rack\n rack[-1] = False\n return\n\n def parse_well(well):\n letter = well[0]\n number = well[1:]\n return letter.upper() + str(int(number))\n\n # import pdb; pdb.set_trace()\n if tip_reuse == 'always':\n try:\n pick_up(pip)\n except OutOfTipsError:\n # Try again after tipracks are reset\n pick_up(pip)\n for line in transfer_info:\n s_well, h, d_well, vol = line[:4]\n source_locn = \\\n source_plate.wells_by_name()[parse_well(s_well)].bottom(float(h))\n dest_locn = \\\n dest_plate.wells_by_name()[parse_well(d_well)]\n if tip_reuse == 'never':\n try:\n pick_up(pip)\n except OutOfTipsError:\n # Try again after tipracks are reset\n pick_up(pip)\n # pip.transfer(float(vol), source_locn, dest_locn, new_tip='never')\n pip.aspirate(float(vol), source_locn)\n pip.dispense(float(vol), dest_locn)\n if tip_reuse == 'never':\n pip.drop_tip()\n if pip.has_tip:\n pip.drop_tip()\n", + "content": "from opentrons import protocol_api\nfrom opentrons.protocol_api.labware import OutOfTipsError\nfrom opentrons.types import Mount\n\n\nmetadata = {\n 'protocolName':\n ('Cherrypicking with multi-channel pipette substituting for a single '\n 'channel pipette'),\n 'author': 'Nick & Eskil ',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.12'\n}\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n\n [transfer_csv,\n lw_source_plate,\n lw_source_plate_open,\n lw_dest_plate,\n lw_dest_plate_open,\n res_type,\n pipette_type,\n pipette_mount,\n tip_type,\n tip_reuse,\n starting_tiprack_slot,\n starting_tip_well] = get_values( # noqa: F821\n \"transfer_csv\",\n \"lw_source_plate\",\n \"lw_source_plate_open\",\n \"lw_dest_plate\",\n \"lw_dest_plate_open\",\n \"res_type\",\n \"pipette_type\",\n \"pipette_mount\",\n \"tip_type\",\n \"tip_reuse\",\n \"starting_tiprack_slot\",\n \"starting_tip_well\")\n\n tiprack_map = {\n 'p20_multi_gen2': {\n 'standard': 'opentrons_96_tiprack_20ul',\n 'filter': 'opentrons_96_filtertiprack_20ul'\n },\n 'p300_multi_gen2': {\n 'standard': 'opentrons_96_tiprack_300ul',\n 'filter': 'opentrons_96_filtertiprack_200ul'\n }\n }\n\n # Parse csv\n # Format: Source Well, Source Aspiration Height Above Bottom (in mm),\n # Dest Well, Vol (in ul)\n transfer_info = [[val.strip().lower() for val in line.split(',')]\n for line in transfer_csv.splitlines()\n if line.split(',')[0].strip()][1:]\n\n if lw_source_plate_open.strip():\n lw_source_plate_name = lw_source_plate_open\n else:\n lw_source_plate_name = lw_source_plate\n if lw_dest_plate_open.strip():\n lw_dest_plate_name = lw_dest_plate_open\n else:\n lw_dest_plate_name = lw_dest_plate\n\n # Load labware\n # Plate to cherrypick from\n source_plate = ctx.load_labware(lw_source_plate_name, '7')\n dest_plate = ctx.load_labware(lw_dest_plate_name, '8')\n # This reservoir is unused, but present\n if res_type != \"none\":\n ctx.load_labware(res_type, '9')\n\n # Load tipracks\n tip_name = tiprack_map[pipette_type][tip_type]\n tiprack_slots = ['4', '5', '10', '11']\n tipracks = [ctx.load_labware(tip_name, slot)\n for slot in tiprack_slots]\n\n # load pipette\n pip = ctx.load_instrument(pipette_type, pipette_mount, tip_racks=tipracks)\n\n if not ctx.is_simulating():\n pick_up_current = 0.1 # 100 mA for single tip\n # Uncomment the next two lines if using Opentrons Robot Software version 7.1.x. # noqa: E501\n # Comment them if NOT using 7.1.x\n\n ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pip.mount)).update_config_item( # noqa: E501\n {'pick_up_current': {8: pick_up_current}})\n\n # Uncomment the next two lines if using Opentrons Robot Software version 7.2.x # noqa: E501\n # Comment them if NOT using 7.2.x\n\n # ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pip.mount)).update_config_item(\n # {'pick_up_current': pick_up_current})\n\n # Tip_map has the columns reversed, pipette always picks up the\n # bottom-most tip in a given column until the column is depleted, and then\n # moves to the next column (from left to right).\n tip_map = []\n for rack in tipracks:\n tip_map.append(\n [[col for col in reversed(column)] for column in rack.columns()])\n # Flag at the end of each rack that is true if there are tips left\n for rack in tip_map:\n rack.append(True)\n # Flag used tipracks based on the protocol input parameter.\n # Check that the input parameter is an existing tiprack slot\n if starting_tiprack_slot not in tiprack_slots:\n raise Exception(\n f\"The Starting Tiprack Slot ({starting_tiprack_slot}) is invalid \"\n f\"The valid tiprack slots are {tiprack_slots}\"\n )\n start_rack_index = tiprack_slots.index(starting_tiprack_slot)\n for i in range(start_rack_index):\n tip_map[i][-1] = False\n\n # Flag used tips in the first available tiprack\n for column in tip_map[start_rack_index]:\n is_break = False\n for well in column:\n if well.well_name != starting_tip_well:\n well.has_tip = False\n else:\n is_break = True\n break\n if is_break:\n break\n\n def pick_up(pipette):\n \"\"\"`pick_up()` will pause the ctx when all tip boxes are out of\n tips, prompting the user to replace all tip racks. Once tipracks are\n reset, the ctx will start picking up tips from the first tip\n box as defined in the slot order when assigning the labware definition\n for that tip box. `pick_up()` will track tips for both pipettes if\n applicable.\n\n :param pipette: The pipette desired to pick up tip\n as definited earlier in the ctx (e.g. p300, m20).\n \"\"\"\n for i, rack in enumerate(tip_map):\n # Check the flag to see if the rack is empty, then we don't loop\n # through that rack so that the algorithm executes faster.\n if rack[-1] is False:\n if i == len(tip_map) - 1: # All tips are used, time to reset\n ctx.pause(\"Replace empty tip racks\")\n # print(\"Replace empty tip racks\")\n pipette.reset_tipracks()\n for rack in tip_map:\n rack[-1] = True\n # Raise an exception so that we can retry the pick up\n raise OutOfTipsError(\n \"Tipracks were out of tips and were reset\")\n else:\n continue\n for column in rack[:-1]: # skip [-1] index because it's the flag\n for well in column:\n if well.has_tip:\n pipette.pick_up_tip(well)\n if well.well_name == 'A12': # last tip in the rack\n rack[-1] = False\n return\n\n def parse_well(well):\n letter = well[0]\n number = well[1:]\n return letter.upper() + str(int(number))\n\n # import pdb; pdb.set_trace()\n if tip_reuse == 'always':\n try:\n pick_up(pip)\n except OutOfTipsError:\n # Try again after tipracks are reset\n pick_up(pip)\n for line in transfer_info:\n s_well, h, d_well, vol = line[:4]\n source_locn = \\\n source_plate.wells_by_name()[parse_well(s_well)].bottom(float(h))\n dest_locn = \\\n dest_plate.wells_by_name()[parse_well(d_well)]\n if tip_reuse == 'never':\n try:\n pick_up(pip)\n except OutOfTipsError:\n # Try again after tipracks are reset\n pick_up(pip)\n # pip.transfer(float(vol), source_locn, dest_locn, new_tip='never')\n pip.aspirate(float(vol), source_locn)\n pip.dispense(float(vol), dest_locn)\n if tip_reuse == 'never':\n pip.drop_tip()\n if pip.has_tip:\n pip.drop_tip()\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/6d901d-2/README.json b/protoBuilds/6d901d-2/README.json index 863a88b36..4f005a893 100644 --- a/protoBuilds/6d901d-2/README.json +++ b/protoBuilds/6d901d-2/README.json @@ -6,16 +6,16 @@ ] }, "deck-setup": "\nExample deck setup.\n\n\n", - "description": "A protocol based on our most robust cherrypicking protocol that has been modified to use a multi-channel pipette as single channel by only picking up a single tip at a time. Specify aspiration height, pipette, as well as source and destination wells with this all inclusive cherrypicking protocol.\nThis is an optional Part 2 protocol to its corresponding Part 1: Normalization protocol using a multi-channel pipette\nNote: This protocol was updated for a change in our software stack and will require app 6.0 or greater.\n\nExplanation of complex parameters below:\n\ninput .csv file: Here, you should upload a .csv file formatted in the following way, making sure to include headers in your csv file.\nSource Plate Type: The plate that you want to cherrypick samples from.\nDestination Plate Type: The plate that you want to dispense cherrypicked samples in.\nReservoir Type: A placeholder from part 1 of this protocol, it should be the same as the reservoir from part 1, although it is not used in this protocol. If there is no reservoir present in slot 9 you can set it to None.\nPipette Model: Select which pipette you will use for this protocol.\nPipette Mount: Specify which mount your multi-channel pipette is on (left or right)\nTip Type: Specify whether you want to use filter- or regular tips.\nTip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.\nStarting Tiprack Slot: If you want to start this protocol right after finishing part 1 without replacing your tipracks you can designate the first non-empty tiprack on the deck to start picking up tips from, otherwise leave this parameter at its default value of slot 4. The tipracks are ordered from first to last as slot 4, 5, 10, and 11.\nStarting Tip Well: Indicate the first well of the first non-empty tiprack containing a tip, e.g. H5, or B3, etc. Leave this parameter with the default value of H1 if starting with fresh tipracks.\n\n", + "description": "A protocol based on our most robust cherrypicking protocol that has been modified to use a multi-channel pipette as single channel by only picking up a single tip at a time. Specify aspiration height, pipette, as well as source and destination wells with this all inclusive cherrypicking protocol.\nThis is an optional Part 2 protocol to its corresponding Part 1: Normalization protocol using a multi-channel pipette\nNote: This protocol was updated for a change in our software stack and will require app 7.0 or greater.\n\nExplanation of complex parameters below:\n\ninput .csv file: Here, you should upload a .csv file formatted in the following way, making sure to include headers in your csv file.\nSource Plate Type: The plate that you want to cherrypick samples from.\nDestination Plate Type: The plate that you want to dispense cherrypicked samples in.\nReservoir Type: A placeholder from part 1 of this protocol, it should be the same as the reservoir from part 1, although it is not used in this protocol. If there is no reservoir present in slot 9 you can set it to None.\nPipette Model: Select which pipette you will use for this protocol.\nPipette Mount: Specify which mount your multi-channel pipette is on (left or right)\nTip Type: Specify whether you want to use filter- or regular tips.\nTip Usage Strategy: Specify whether you'd like to use a new tip for each transfer, or keep the same tip throughout the protocol.\nStarting Tiprack Slot: If you want to start this protocol right after finishing part 1 without replacing your tipracks you can designate the first non-empty tiprack on the deck to start picking up tips from, otherwise leave this parameter at its default value of slot 4. The tipracks are ordered from first to last as slot 4, 5, 10, and 11.\nStarting Tip Well: Indicate the first well of the first non-empty tiprack containing a tip, e.g. H5, or B3, etc. Leave this parameter with the default value of H1 if starting with fresh tipracks.\n\n", "internal": "6d901d-2", - "labware": "\nAny verified labware found in our Labware Library and some additional microplates (see plate options for source and destination plates parameters below, e.g. Greiner Bio-One plates)\n", + "labware": "\nAny verified labware found in our Labware Library and some additional microplates (see plate options for source and destination plates parameters below, e.g. Greiner Bio-One plates).\n", "markdown": { "author": "[Opentrons](https://opentrons.com/)\n\n", "categories": "* Sample Prep\n\t* Cherrypicking\n\n", "deck-setup": "* Example deck setup.\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6d901d/2/example_deck.jpg)\n\n---\n\n", - "description": "\nA protocol based on our most robust [cherrypicking protocol](https://protocols.opentrons.com/protocol/cherrypicking) that has been modified to use a multi-channel pipette as single channel by only picking up a single tip at a time. Specify aspiration height, pipette, as well as source and destination wells with this all inclusive cherrypicking protocol.\n\nThis is an optional Part 2 protocol to its corresponding [Part 1: Normalization protocol using a multi-channel pipette](https://protocols.opentrons.com/protocol/6d901d)\n\n**Note**: This protocol was updated for a change in our software stack and will require app 6.0 or greater.\n\n![Cherrypicking Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/cherrypicking/cherrypicking_example.png)\n\nExplanation of complex parameters below:\n\n* `input .csv file`: Here, you should upload a .csv file formatted in the [following way](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6d901d/2/example.csv), making sure to include headers in your csv file.\n* `Source Plate Type`: The plate that you want to cherrypick samples from.\n* `Destination Plate Type`: The plate that you want to dispense cherrypicked samples in.\n* `Reservoir Type`: A placeholder from part 1 of this protocol, it should be the same as the reservoir from part 1, although it is not used in this protocol. If there is no reservoir present in slot 9 you can set it to None.\n* `Pipette Model`: Select which pipette you will use for this protocol.\n* `Pipette Mount`: Specify which mount your multi-channel pipette is on (left or right)\n* `Tip Type`: Specify whether you want to use filter- or regular 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.\n* `Starting Tiprack Slot`: If you want to start this protocol right after finishing part 1 without replacing your tipracks you can designate the first non-empty tiprack on the deck to start picking up tips from, otherwise leave this parameter at its default value of slot 4. The tipracks are ordered from first to last as slot 4, 5, 10, and 11.\n* `Starting Tip Well`: Indicate the first well of the first non-empty tiprack containing a tip, e.g. H5, or B3, etc. Leave this parameter with the default value of H1 if starting with fresh tipracks.\n\n---\n\n", + "description": "\nA protocol based on our most robust [cherrypicking protocol](https://protocols.opentrons.com/protocol/cherrypicking) that has been modified to use a multi-channel pipette as single channel by only picking up a single tip at a time. Specify aspiration height, pipette, as well as source and destination wells with this all inclusive cherrypicking protocol.\n\nThis is an optional Part 2 protocol to its corresponding [Part 1: Normalization protocol using a multi-channel pipette](https://protocols.opentrons.com/protocol/6d901d)\n\n**Note**: This protocol was updated for a change in our software stack and will require app 7.0 or greater.\n\n![Cherrypicking Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/cherrypicking/cherrypicking_example.png)\n\nExplanation of complex parameters below:\n\n* `input .csv file`: Here, you should upload a .csv file formatted in the [following way](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6d901d/2/example.csv), making sure to include headers in your csv file.\n* `Source Plate Type`: The plate that you want to cherrypick samples from.\n* `Destination Plate Type`: The plate that you want to dispense cherrypicked samples in.\n* `Reservoir Type`: A placeholder from part 1 of this protocol, it should be the same as the reservoir from part 1, although it is not used in this protocol. If there is no reservoir present in slot 9 you can set it to None.\n* `Pipette Model`: Select which pipette you will use for this protocol.\n* `Pipette Mount`: Specify which mount your multi-channel pipette is on (left or right)\n* `Tip Type`: Specify whether you want to use filter- or regular 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.\n* `Starting Tiprack Slot`: If you want to start this protocol right after finishing part 1 without replacing your tipracks you can designate the first non-empty tiprack on the deck to start picking up tips from, otherwise leave this parameter at its default value of slot 4. The tipracks are ordered from first to last as slot 4, 5, 10, and 11.\n* `Starting Tip Well`: Indicate the first well of the first non-empty tiprack containing a tip, e.g. H5, or B3, etc. Leave this parameter with the default value of H1 if starting with fresh tipracks.\n\n---\n\n", "internal": "6d901d-2\n", - "labware": "* Any verified labware found in our [Labware Library](https://labware.opentrons.com/?category=wellPlate) and some additional microplates (see plate options for source and destination plates parameters below, e.g. Greiner Bio-One plates)\n\n", + "labware": "* Any verified labware found in our [Labware Library](https://labware.opentrons.com/?category=wellPlate) and some additional microplates (see plate options for source and destination plates parameters below, e.g. Greiner Bio-One plates).\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", "partner": "[AstraZeneca](https://www.astrazeneca.com/)\n\n\n\n", "pipettes": "* [P20 Multi GEN2 Pipette](https://shop.opentrons.com/8-channel-electronic-pipette/)\n* [P300 Multi GEN2 Pipette](https://shop.opentrons.com/8-channel-electronic-pipette/)\n\n---\n\n", diff --git a/protoBuilds/6d901d/6d901d.ot2.apiv2.py.json b/protoBuilds/6d901d/6d901d.ot2.apiv2.py.json index f7bdf347f..e67fb0c9d 100644 --- a/protoBuilds/6d901d/6d901d.ot2.apiv2.py.json +++ b/protoBuilds/6d901d/6d901d.ot2.apiv2.py.json @@ -1,5 +1,5 @@ { - "content": "from opentrons import protocol_api\nfrom opentrons import types\n\nmetadata = {\n 'protocolName': 'Normalization with a multi-channel pipette \\\n used as a single-channel pipette',\n 'author': 'Opentrons ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.12'\n }\n\n\ndef transpose_matrix(m):\n return [[r[i] for r in reversed(m)] for i in range(len(m[0]))]\n\n\ndef flatten_matrix(m):\n \"\"\" Converts a matrix to a 1D array, e.g. [[1,2],[3,4]] -> [1,2,3,4]\n \"\"\"\n return [cell for row in m for cell in row]\n\n\ndef well_csv_to_list(csv_string):\n \"\"\"\n Takes a csv string and flattens it to a list, re-ordering to match\n Opentrons well order convention (A1, B1, C1, ..., A2, B2, B2, ...)\n \"\"\"\n data = [\n line.split(',')\n for line in reversed(csv_string.split('\\n')) if line.strip()\n if line\n ]\n if len(data[0]) > len(data):\n # row length > column length ==> \"landscape\", so transpose\n return flatten_matrix(transpose_matrix(data))\n # \"portrait\"\n return flatten_matrix(data)\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n [volumes_csv,\n p300_mount,\n p20_mount,\n plate_type,\n res_type,\n filter_tip,\n tip_reuse] = get_values( # noqa: F821\n \"volumes_csv\",\n \"p300_mount\",\n \"p20_mount\",\n \"plate_type\",\n \"res_type\",\n \"filter_tip\",\n \"tip_reuse\")\n\n # create labware\n source_plate = ctx.load_labware(plate_type, '7')\n # There could be a destination plate in slot 8 for cherry picking\n # Load something tall so the pipette doesn't hit it\n ctx.load_labware('usascientific_96_wellplate_2.4ml_deep', '8')\n reservoir = ctx.load_labware(res_type, '9')\n source = reservoir.wells()[0]\n if filter_tip:\n tips300 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '10')\n tips20 = ctx.load_labware('opentrons_96_filtertiprack_20ul', '11')\n else:\n tips300 = ctx.load_labware('opentrons_96_tiprack_300ul', '10')\n tips20 = ctx.load_labware('opentrons_96_tiprack_20ul', '11')\n\n m300 = ctx.load_instrument('p300_multi_gen2', p300_mount)\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount)\n\n mounted_on = {\"left\": types.Mount.LEFT, \"right\": types.Mount.RIGHT}\n\n pick_up_current = 0.15 # 150 mA for single tip\n ctx._hw_manager.hardware._attached_instruments[\n mounted_on[m20.mount]].update_config_item(\n 'pick_up_current', pick_up_current)\n\n tip300ctr = 95\n tip20ctr = 95\n\n def pick_up(pip):\n \"\"\"`pick_up()` will pause the ctx when all tip boxes are out of\n tips, prompting the user to replace all tip racks. Once tipracks are\n reset, the ctx will start picking up tips from the first tip\n box as defined in the slot order when assigning the labware definition\n for that tip box. `pick_up()` will track tips for both pipettes if\n applicable.\n\n :param pipette: The pipette desired to pick up tip\n as definited earlier in the ctx (e.g. p300, m20).\n \"\"\"\n nonlocal tip300ctr\n nonlocal tip20ctr\n\n if pip == m300:\n if tip300ctr < 0:\n ctx.home()\n ctx.pause('Please replace tips for P300 in slot 10.')\n tip300ctr = 95\n m300.pick_up_tip(tips300.wells()[tip300ctr])\n tip300ctr -= 1\n else:\n if tip20ctr < 0:\n ctx.home()\n ctx.pause('Please replace tips for P20 in slot 11.')\n tip20ctr = 95\n m20.pick_up_tip(tips20.wells()[tip20ctr])\n tip20ctr -= 1\n\n # create volumes list\n volumes = [float(cell) for cell in well_csv_to_list(volumes_csv)]\n\n is_warning = False\n\n for vol in volumes:\n if vol < 1:\n ctx.comment(\n 'WARNING: volume {} is below pipette\\'s minimum volume.'\n .format(vol))\n is_warning = True\n\n if is_warning:\n ctx.comment(\"\\n\")\n ctx.pause(\n \"One or more minimum volume warnings were detected \"\n \"Do you wish to continue?\\n\")\n\n for i, vol in enumerate(volumes):\n pipette = m20 if vol <= 20 else m300\n if not pipette.has_tip:\n pick_up(pipette)\n if vol != 0:\n pipette.aspirate(vol, source)\n pipette.dispense(vol, source_plate.wells()[i])\n if tip_reuse == 'never':\n pipette.drop_tip()\n", + "content": "from opentrons import protocol_api\nfrom opentrons.types import Mount\n\nmetadata = {\n 'protocolName': 'Normalization with a multi-channel pipette \\\n used as a single-channel pipette',\n 'author': 'Opentrons ',\n 'source': 'Protocol Library',\n 'apiLevel': '2.12'\n }\n\n\ndef transpose_matrix(m):\n return [[r[i] for r in reversed(m)] for i in range(len(m[0]))]\n\n\ndef flatten_matrix(m):\n \"\"\" Converts a matrix to a 1D array, e.g. [[1,2],[3,4]] -> [1,2,3,4]\n \"\"\"\n return [cell for row in m for cell in row]\n\n\ndef well_csv_to_list(csv_string):\n \"\"\"\n Takes a csv string and flattens to a list, re-ordering to match\n Opentrons well order convention (A1, B1, C1, ..., A2, B2, B2, ...)\n \"\"\"\n data = [\n line.split(',')\n for line in reversed(csv_string.split('\\n')) if line.strip()\n if line\n ]\n if len(data[0]) > len(data):\n # row length > column length ==> \"landscape\", so transpose\n return flatten_matrix(transpose_matrix(data))\n # \"portrait\"\n return flatten_matrix(data)\n\n\ndef run(ctx: protocol_api.ProtocolContext):\n [volumes_csv,\n p300_mount,\n p20_mount,\n plate_type,\n res_type,\n filter_tip,\n tip_reuse] = get_values( # noqa: F821\n \"volumes_csv\",\n \"p300_mount\",\n \"p20_mount\",\n \"plate_type\",\n \"res_type\",\n \"filter_tip\",\n \"tip_reuse\")\n\n # create labware\n source_plate = ctx.load_labware(plate_type, '7')\n # There could be a destination plate in slot 8 for cherry picking\n # Load something tall so the pipette doesn't hit it\n ctx.load_labware('usascientific_96_wellplate_2.4ml_deep', '8')\n reservoir = ctx.load_labware(res_type, '9')\n source = reservoir.wells()[0]\n if filter_tip:\n tips300 = ctx.load_labware('opentrons_96_filtertiprack_200ul', '10')\n tips20 = ctx.load_labware('opentrons_96_filtertiprack_20ul', '11')\n else:\n tips300 = ctx.load_labware('opentrons_96_tiprack_300ul', '10')\n tips20 = ctx.load_labware('opentrons_96_tiprack_20ul', '11')\n\n m300 = ctx.load_instrument('p300_multi_gen2', p300_mount)\n m20 = ctx.load_instrument('p20_multi_gen2', p20_mount)\n\n if not ctx.is_simulating():\n pick_up_current = 0.1 # 100 mA for single tip\n # Uncomment the next two lines if using Opentrons Robot Software version 7.1.x. # noqa:E501\n # Comment them if NOT using 7.1.x\n for pipette in [m20, m300]:\n ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pipette.mount)).update_config_item( # noqa:E501\n {'pick_up_current': {8: pick_up_current}})\n\n # Uncomment the next two lines if using Opentrons Robot Software version 7.2.x # noqa:E501\n # Comment them if NOT using 7.2.x\n # for pipette in [m20, m300]:\n # ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pipette.mount)).update_config_item(\n # {'pick_up_current': pick_up_current})\n\n tip300ctr = 95\n tip20ctr = 95\n\n def pick_up(pip):\n \"\"\"`pick_up()` will pause the ctx when all tip boxes are out of\n tips, prompting the user to replace all tip racks. Once tipracks are\n reset, the ctx will start picking up tips from the first tip\n box as defined in the slot order when assigning the labware definition\n for that tip box. `pick_up()` will track tips for both pipettes if\n applicable.\n\n :param pipette: The pipette desired to pick up tip\n as definited earlier in the ctx (e.g. p300, m20).\n \"\"\"\n nonlocal tip300ctr\n nonlocal tip20ctr\n\n if pip == m300:\n if tip300ctr < 0:\n ctx.home()\n ctx.pause('Please replace tips for P300 in slot 10.')\n tip300ctr = 95\n m300.pick_up_tip(tips300.wells()[tip300ctr])\n tip300ctr -= 1\n else:\n if tip20ctr < 0:\n ctx.home()\n ctx.pause('Please replace tips for P20 in slot 11.')\n tip20ctr = 95\n m20.pick_up_tip(tips20.wells()[tip20ctr])\n tip20ctr -= 1\n\n # create volumes list\n volumes = [float(cell) for cell in well_csv_to_list(volumes_csv)]\n\n is_warning = False\n\n for vol in volumes:\n if vol < 1:\n ctx.comment(\n 'WARNING: volume {} is below pipette\\'s minimum volume.'\n .format(vol))\n is_warning = True\n\n if is_warning:\n ctx.comment(\"\\n\")\n ctx.pause(\n \"One or more minimum volume warnings were detected \"\n \"Do you wish to continue?\\n\")\n\n for i, vol in enumerate(volumes):\n pipette = m20 if vol <= 20 else m300\n if not pipette.has_tip:\n pick_up(pipette)\n if vol != 0:\n pipette.aspirate(vol, source)\n pipette.dispense(vol, source_plate.wells()[i])\n if tip_reuse == 'never':\n pipette.drop_tip()\n", "custom_labware_defs": [ { "brand": { diff --git a/protoBuilds/6d901d/README.json b/protoBuilds/6d901d/README.json index 9d73bbebf..f24800a91 100644 --- a/protoBuilds/6d901d/README.json +++ b/protoBuilds/6d901d/README.json @@ -6,13 +6,13 @@ ] }, "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 requires app 7.0 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", "categories": "* Sample Prep\n\t* Normalization with a multi-channel pipette substituting for a single-channel pipette\n\n\n", "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![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/6d901d/example_deck.jpg)\n* Well A1 on the reservoir on slot 9: Diluent, e.g. water or buffer.\n\n", - "description": "![Normalization Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/normalization/normalization_example.png)\n\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](https://protocols.opentrons.com/protocol/normalization), that instead uses a multi-channel pipette as single channel pipette by picking up one tip at a time.\n\nThere is an optional [Part 2: Cherrypicking Protocol](https://protocols.opentrons.com/protocol/6d901d-2) to this protocol which performs cherrypicking using a multi-channel pipette in the same way.\n\n**Note**: This protocol was updated for a change in our software stack and will require app 6.0 or greater.\n\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---\n\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 4.4.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons Multi-Channel Pipette](https://shop.opentrons.com/8-channel-electronic-pipette/) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips)\n* [Samples in a compatible plate (96-well or 384-well)](https://labware.opentrons.com/?category=wellPlate)\n* [Automation-friendly reservoir](https://labware.opentrons.com/?category=reservoir)\n* Diluent\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n---\n\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\n**CSV Format**\n\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\n![Normalization CSV](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/normalization/normalization_csv.png)\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, etc.\n\nIf you would like to follow our template, you can make a copy of [this spreadsheet](https://opentrons-protocol-library-website.s3.amazonaws.com/Technical+Notes/normalization/Opentrons+Normalization+Template.xlsx), fill out your values, and export as CSV from there.\n\n*Note 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\n", + "description": "![Normalization Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/normalization/normalization_example.png)\n\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](https://protocols.opentrons.com/protocol/normalization), that instead uses a multi-channel pipette as single channel pipette by picking up one tip at a time.\n\nThere is an optional [Part 2: Cherrypicking Protocol](https://protocols.opentrons.com/protocol/6d901d-2) to this protocol which performs cherrypicking using a multi-channel pipette in the same way.\n\n**Note**: This protocol was updated for a change in our software stack and requires app 7.0 or greater.\n\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---\n\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 4.4.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons Multi-Channel Pipette](https://shop.opentrons.com/8-channel-electronic-pipette/) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips)\n* [Samples in a compatible plate (96-well or 384-well)](https://labware.opentrons.com/?category=wellPlate)\n* [Automation-friendly reservoir](https://labware.opentrons.com/?category=reservoir)\n* Diluent\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n---\n\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\n**CSV Format**\n\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\n![Normalization CSV](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/normalization/normalization_csv.png)\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, etc.\n\nIf you would like to follow our template, you can make a copy of [this spreadsheet](https://opentrons-protocol-library-website.s3.amazonaws.com/Technical+Notes/normalization/Opentrons+Normalization+Template.xlsx), fill out your values, and export as CSV from there.\n\n*Note 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\n", "internal": "6d901d\n", "notes": "\nIf you\u2019d like to request a protocol supporting multiple plates or require any other changes to this script, please fill out our [Protocol Request Form](https://opentrons-protocol-dev.paperform.co/). You can also modify the Python file directly by following our [API Documentation](https://docs.opentrons.com/v2/). If you\u2019d like to chat with an applications engineer about changes, please contact us at [protocols@opentrons.com](mailto:protocols@opentrons.com).\n\n", "partner": "[AstraZeneca](https://www.astrazeneca.com/)\n\n\n\n", diff --git a/protoBuilds/Opentrons_Logo/README.json b/protoBuilds/Opentrons_Logo/README.json index bbeb49d18..5137a9408 100644 --- a/protoBuilds/Opentrons_Logo/README.json +++ b/protoBuilds/Opentrons_Logo/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Getting Started": [ "Opentrons Logo" @@ -8,7 +8,7 @@ "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# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/opentrons_logo). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Getting Started\n\t* Opentrons Logo\n\n", "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---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons Single-Channel Pipette](https://shop.opentrons.com/collections/ot-2-pipettes) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips)\n* [96-Well Microplate](https://labware.opentrons.com/?category=wellPlate)\n* [12-Row Trough](https://labware.opentrons.com/?category=reservoir) or [Tube Rack with 1.5mL/2mL Tubes](https://labware.opentrons.com/?category=tubeRack)\n* Water and Food Dye (Two Colors)\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\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.\n\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'.\n\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.\n\n\n", "internal": "Demo Protocol 1\n", diff --git a/protoBuilds/cherrypicking/README.json b/protoBuilds/cherrypicking/README.json index 2ea47b077..189761b3d 100644 --- a/protoBuilds/cherrypicking/README.json +++ b/protoBuilds/cherrypicking/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Featured": [ "Cherrypicking" @@ -10,7 +10,7 @@ "internal": "cherrypicking", "labware": "\nAny verified labware found in our Labware Library\n", "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/cherrypicking). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Featured\n\t* Cherrypicking\n\n", "deck-setup": "* Example deck setup - tip racks loaded onto remining slots.\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/cherrypicking/Screen+Shot+2021-04-29+at+3.10.02+PM.png)\n\n---\n\n", "description": "\nOur most robust cherrypicking protocol. Specify aspiration height, labware, pipette, as well as source and destination wells with this all inclusive cherrypicking protocol.\n\n![Cherrypicking Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/cherrypicking/cherrypicking_example.png)\n\nExplanation of complex parameters below:\n\n* `input .csv file`: Here, you should upload a .csv file formatted in the [following way](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/1211/example.csv), making sure to include headers in your csv file. Refer to our [Labware Library](https://labware.opentrons.com/?category=wellPlate) to copy API names for labware to include in the `Source Labware` and `Dest Labware` columns of the .csv.\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.\n\n\n\n---\n\n\n", diff --git a/protoBuilds/customizable_serial_dilution_ot2/README.json b/protoBuilds/customizable_serial_dilution_ot2/README.json index 6c7f6a92f..d3571b576 100644 --- a/protoBuilds/customizable_serial_dilution_ot2/README.json +++ b/protoBuilds/customizable_serial_dilution_ot2/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Featured": [ "Serial Dilution" @@ -8,7 +8,7 @@ "description": "With this protocol, you can do a simple serial dilution across a 96-well plate using either a single-channel or 8-channel pipette. This can be useful for everything from creating a simple standard curve to a concentration-limiting dilution. For more information (including data from the Opentrons Lab and other considerations), please see our Technical Note.\n\n\n\nExample Setup\nThis protocol uses the inputs you define for \"Dilution Factor\" and \"Total Mixing Volume\" to automatically infer the necessary transfer volume for each dilution across your plate. For a 1 in 3 dilution series across an entire plate, as seen above:\n-- Start with your samples/reagents in Column 1 of your plate. In this example, you would pre-add 150 uL of concentrated sample to the first column of your 96-well plate.\n-- Define a Total Mixing Volume of 150uL, a Dilution Factor of 3, and set Number of Dilutions = 11.\n-- Your OT-2 will add 100uL of diluent to each empty well in your plate. Then it will transfer 50uL from Column 1 between each well/column in the plate.\n-- \"Total mixing volume\" = transfer volume + diluent volume.\n\n\n\n-- Opentrons OT-2\n-- Opentrons OT-2 Run App (Version 3.19 or later)\n-- Opentrons Tips for selected Opentrons Pipette\n-- 12-Row, Automation-Friendly Trough\n-- 96-Well Plate (found in our Labware Library)\n-- Diluent (Pre-loaded in row 1 of trough)\n-- Samples/Standards (Pre-loaded in Column 1 of a standard 96-well plate)", "internal": "Customizable Serial Dilution, v2", "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/customizable_serial_dilution_ot2). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Featured\n * Serial Dilution\n\n", "description": "With this protocol, you can do a simple serial dilution across a 96-well plate using either a single-channel or 8-channel pipette. This can be useful for everything from creating a simple standard curve to a concentration-limiting dilution. For more information (including data from the Opentrons Lab and other considerations), please see our [Technical Note](https://s3.amazonaws.com/opentrons-protocol-library-website/Technical+Notes/Serial+Dilution+OT2+Technical+Note.pdf).\n\n---\n\n---\n\n![serial dilution](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/customizable-serial-dilution/Customizable+Serial+Dilution+Illustration+LATEST+VERSION.jpg)\n\nExample Setup\n\nThis protocol uses the inputs you define for \"Dilution Factor\" and \"Total Mixing Volume\" to automatically infer the necessary transfer volume for each dilution across your plate. For a 1 in 3 dilution series across an entire plate, as seen above:\n\n-- Start with your samples/reagents in Column 1 of your plate. In this example, you would pre-add 150 uL of concentrated sample to the first column of your 96-well plate.\n\n-- Define a Total Mixing Volume of 150uL, a Dilution Factor of 3, and set Number of Dilutions = 11.\n\n-- Your OT-2 will add 100uL of diluent to each empty well in your plate. Then it will transfer 50uL from Column 1 between each well/column in the plate.\n\n-- \"Total mixing volume\" = transfer volume + diluent volume.\n\n---\n\n---\n\n\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/customizable-serial-dilution/materials.png)\n\n-- [Opentrons OT-2](http://opentrons.com/ot-2)\n\n-- [Opentrons OT-2 Run App (Version 3.19 or later)](http://opentrons.com/ot-app)\n\n-- [Opentrons Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips-racks-9-600-tips) for selected Opentrons Pipette\n\n-- [12-Row, Automation-Friendly Trough](https://shop.opentrons.com/nest-12-well-reservoirs-15-ml/)\n\n-- [96-Well Plate](https://shop.opentrons.com/nest-96-well-plate-flat/) (found in our [Labware Library](https://labware.opentrons.com/?category=wellPlate))\n\n-- Diluent (Pre-loaded in row 1 of trough)\n\n-- Samples/Standards (Pre-loaded in Column 1 of a standard 96-well plate)\n\n", "internal": "Customizable Serial Dilution, v2\n", diff --git a/protoBuilds/dinosaur/README.json b/protoBuilds/dinosaur/README.json index 5e5e2993e..8905c3e4b 100644 --- a/protoBuilds/dinosaur/README.json +++ b/protoBuilds/dinosaur/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Getting Started": [ "Dinosaur" @@ -8,7 +8,7 @@ "description": "Draw a picture of a dinosaur (Stegosaurus!) on a 96 well plate using food coloring.\n\n\n\n\nOpentrons 300uL Tips\nOpentrons 200uL Filter Tips\nBio-Rad 96 Well Plate 200 uL PCR\nNEST 96 Well Plate 100 uL PCR Full Skirt\nCorning 96 Well Plate 360 \u00b5L Flat\nNEST 96 Well Plate 200 \u00b5L Flat\nP300 Single Channel GEN2\n\nFor more detailed information on compatible labware, please visit our Labware Library.\n\n\nDeck Setup\n\nProtocol Steps\n\nDistribute 50 uL of green solution to all the necessary wells.\nDistribute 50 uL of blue solution to all the necessary wells.\nEnjoy the dinosaur!\n", "internal": "dinosaur", "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/dinosaur). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Getting Started\n\t* Dinosaur\n\n", "description": "Draw a picture of a dinosaur (Stegosaurus!) on a 96 well plate using food coloring.\n\n![Dinosaur](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/dinosaur/dinosaur_result.png)\n\n---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\n* [Opentrons 300uL Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-200ul-filter-tips)\n* [Opentrons 200uL Filter Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-200ul-filter-tips)\n* [Bio-Rad 96 Well Plate 200 uL PCR](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr/)\n* [NEST 96 Well Plate 100 uL PCR Full Skirt](https://labware.opentrons.com/nest_96_wellplate_100ul_pcr_full_skirt/)\n* [Corning 96 Well Plate 360 \u00b5L Flat](https://labware.opentrons.com/corning_96_wellplate_360ul_flat/)\n* [NEST 96 Well Plate 200 \u00b5L Flat](https://labware.opentrons.com/nest_96_wellplate_200ul_flat/)\n* [P300 Single Channel GEN2](https://shop.opentrons.com/collections/ot-2-robot/products/single-channel-electronic-pipette?variant=5984549109789)\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\n**Deck Setup**\n![Deck Layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/dinosaur/dinosaur_deck_layout.png)\n\n\n**Protocol Steps**\n\n1. Distribute 50 uL of green solution to all the necessary wells.\n2. Distribute 50 uL of blue solution to all the necessary wells.\n3. Enjoy the dinosaur!\n\n", "internal": "dinosaur", diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json b/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json index 21665e4d8..ca811b3a4 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part1/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Featured": [ "NGS Library Prep: Illumina Nextera XT" @@ -8,7 +8,7 @@ "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# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/illumina-nextera-xt-library-prep-part1). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Featured\n * NGS Library Prep: Illumina Nextera XT\n\n", "description": "Part 1 of 4: Tagment Genomic DNA and Amplify Libraries\n\nLinks:\n* [Part 1: Tagment and Amplify](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Part 2: Clean Up Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part2)\n* [Part 3: Normalize Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part3)\n* [Part 4: Pool Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part4)\n\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol described by the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-06.pdf).\n\nThis is part 1 of the protocol, which includes the steps (1) Tagment Genomic DNA and (2) Amplify Libraries.\n\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](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-05.pdf).\n\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.\n\n", "internal": "bU7eUGEh\n872\n", diff --git a/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json b/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json index 926d67551..5e77ba26f 100644 --- a/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json +++ b/protoBuilds/illumina-nextera-XT-library-prep-part2/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Featured": [ "NGS Library Prep: Illumina Nextera XT" @@ -8,7 +8,7 @@ "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# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/illumina-nextera-xt-library-prep-part2). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Featured\n * NGS Library Prep: Illumina Nextera XT\n\n", "description": "Part 2 of 4: Clean Up Libraries\n\nLinks:\n* [Part 1: Tagment and Amplify](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Part 2: Clean Up Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part2)\n* [Part 3: Normalize Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part3)\n* [Part 4: Pool Libraries](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part4)\n\nWith this protocol, your robot can perform the Nextera XT DNA Library Prep Kit protocol describe by the [Illumina Reference Guide](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-06.pdf).\n\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.\n\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---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons P300 or P50 Pipette (Single or 8-Channel)](https://shop.opentrons.com/collections/ot-2-pipettes) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* [Opentrons Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n* [Bio-Rad 96-Well Plate, 200\u03bcl](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr) containing samples from [Part 1](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n* [Bio-Rad 96-Well Plate, 200\u03bcl](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr), clean and empty (x2)\n* [USA Scientific 12-Channel Reservoir](https://labware.opentrons.com/usascientific_12_reservoir_22ml?category=reservoir)\n* [Nextera XT DNA Library Prep Kit](https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/nextera-xt-dna.html)\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\nThis protocol requires specific labware in a specific set-up.\n\nSlot 1: [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr?category=wellPlate) (clean and empty); final elution will be transferred to this plate.\n\nSlot 2: [USA Scientific 12-Channel Reservoir](https://labware.opentrons.com/usascientific_12_reservoir_22ml?category=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\n\nSlot 4: [Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck) with [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr?category=wellPlate) (clean and empty)\n\nSlot 5: [Bio-Rad Plate](https://labware.opentrons.com/biorad_96_wellplate_200ul_pcr) containing samples from [Part 1](http://protocols.opentrons.com/protocol/illumina-nextera-XT-library-prep-part1)\n\nSlot 6: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n\nSlot 7: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n\nSlot 8: [Opentrons Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips)\n* Note: If your protocol requires more tips due to the parameters you set, you will need to fill subsequent slots with tip racks.\n\n\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](https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/samplepreps_nextera/nextera-xt/nextera-xt-library-prep-reference-guide-15031942-05.pdf) 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.\n\n\n\n\n\n", "internal": "bU7eUGEh\n872\n", diff --git a/protoBuilds/macherey-nagel-nucleomag-DNA-microbiome/README.json b/protoBuilds/macherey-nagel-nucleomag-DNA-microbiome/README.json index 5f9af1eeb..eecbf60a6 100644 --- a/protoBuilds/macherey-nagel-nucleomag-DNA-microbiome/README.json +++ b/protoBuilds/macherey-nagel-nucleomag-DNA-microbiome/README.json @@ -10,7 +10,7 @@ "internal": "macherey-nagal-nucleomag-dna-microbiome", "labware": "\nMacherey Nagel 96 Well Square Well Block\nMacherey Nagel 96 Well Elution Plate U-bottom\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Generic 2 mL Screwcap\nUSA Scientific 12 Well Reservoir 22 mL #1061-8150\nOpentrons 96 Tip Rack 1000 \u00b5L\nAgilent 1 Well Reservoir 290 mL #201252-100\n", "markdown": { - "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n\n", + "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* MACHEREY-NAGEL NucleoMag\u00ae DNA Microbiome\n\n\n", "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/deck.png)\n\n\n", "description": "![MACHEREY-NAGEL](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/MN_Logo_50.jpeg)\n\nThis protocol automates the NucleoMag\u00ae DNA Microbiome kit for flexible magnetic bead based isolation of DNA from microbiome samples.\n\nBefore beginning the protocol on the OT-2, the following preparation steps are needed.\n1. Perform the lysis according to the NucleoMag\u00ae DNA Microbiome user manual.\n2. Fill the 12-Well Buffer Reservoir according to the table below.\n3. Resuspend the NucleoMag\u00ae B-Beads by vortexing and place them in Position A1 of the 2mL Tube Rack.\n4. Load the instrument deck according to the displayed positions.\n5. Place the Square-well Block containing the lysates on the Magnetic Module and start the run.\n\n\nYou can access the full description of this workflow on the OT-2 by visiting this link: [link](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel-dna-microbiome/line29.pdf)\n\n\n", diff --git a/protoBuilds/macherey-nagel-nucleomag-clean-up/README.json b/protoBuilds/macherey-nagel-nucleomag-clean-up/README.json index 5b06b07c2..8cbe82fea 100644 --- a/protoBuilds/macherey-nagel-nucleomag-clean-up/README.json +++ b/protoBuilds/macherey-nagel-nucleomag-clean-up/README.json @@ -10,7 +10,7 @@ "internal": "macherey-nagel-nucleomag-clean-up", "labware": "\n96 Well PCR Plate\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Generic 2 mL Screwcap\nUSA Scientific 12 Well Reservoir 22 mL #1061-8150\nOpentrons 96 Tip Rack 1000 \u00b5L\n96 Deepwell Plate 2mL\nAgilent 1 Well Reservoir 290 mL #201252-100\n", "markdown": { - "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n\n", + "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n", "categories": "* NGS Library Prep\n\t* MACHEREY-NAGEL Clean-Up\n\n\n", "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/mn-size-select-deck.png)\n\n\n", "description": "![MACHEREY-NAGEL](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/MN_Logo_50.jpeg)\n\nThis protocol automates the MACHEREY-NAGEL NucleoMag\u00ae NGS Clean-Up and allows for flexible parameterization.\n\nBefore beginning the protocol on the OT-2, the following preparation steps are needed:
\n1. Fill the 12-Well Buffer Reservoir according to the table below.\n2. Resuspend the NucleoMag\u00ae NGS Bead suspension by vortexing.\n3. Load the instrument deck according to the displayed positions.\n4. Place the Square-well Block containing the lysates on the Magnetic Module and start the run.\n\nYou can access the full descripition of this workflow on the OT-2 by visiting this link: [link](https://insights.opentrons.com/hubfs/Partners/Macherey-Nagel/NucleoMag%20NGS%20clean-up%20on%20OT-2%20Protocol%20Info.pdf)\n\n\n", diff --git a/protoBuilds/macherey-nagel-nucleomag-dna-food/README.json b/protoBuilds/macherey-nagel-nucleomag-dna-food/README.json index b711c96e6..0720fe1ac 100644 --- a/protoBuilds/macherey-nagel-nucleomag-dna-food/README.json +++ b/protoBuilds/macherey-nagel-nucleomag-dna-food/README.json @@ -10,7 +10,7 @@ "internal": "macherey-nagal-nucleomag-dna-food", "labware": "\nMacherey Nagel 96 Well Square Well Block\nMacherey Nagel 96 Well Elution Plate U-bottom\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Generic 2 mL Screwcap\nUSA Scientific 12 Well Reservoir 22 mL #1061-8150\nOpentrons 96 Tip Rack 1000 \u00b5L\nAgilent 1 Well Reservoir 290 mL #201252-100\n", "markdown": { - "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n\n", + "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* MACHEREY-NAGEL NucleoMag\u00ae DNA Food\n\n\n", "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/deck.png)\n\n\n", "description": "![MACHEREY-NAGEL](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/MN_Logo_50.jpeg)\n\nThis protocol automates the NucleoMag\u00ae DNA Food kit for flexible magnetic bead based isolation of DNA from food samples.\n\nBefore beginning the protocol on the OT-2, the following preparation steps are needed.\n1. Perform the lysis according to the NucleoMag\u00ae DNA Food user manual. Note: We recommend to reduce the sample input to 50mg depending on the sample type.\n2. Fill the 12-Well Buffer Reservoir according to the table below.\n3. Resuspend the NucleoMag\u00ae B-Beads by vortexing and place them in Position A1 of the 2mL Tube Rack.\n4. Load the instrument deck according to the displayed positions.\n5. Place the Square-well Block containing the lysates on the Magnetic Module and start the run.\n\n\nYou can access the full description of this workflow on the OT-2 by visiting this link: [link](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel-dna-food/line29.pdf)\n\n\n", diff --git a/protoBuilds/macherey-nagel-nucleomag-tissue/README.json b/protoBuilds/macherey-nagel-nucleomag-tissue/README.json index a5ace9e87..9eb8bcaec 100644 --- a/protoBuilds/macherey-nagel-nucleomag-tissue/README.json +++ b/protoBuilds/macherey-nagel-nucleomag-tissue/README.json @@ -10,7 +10,7 @@ "internal": "macherey-nagel-nucleomag-tissue", "labware": "\nMacherey Nagel 96 Well Square Well Block\nMacherey Nagel 96 Well Elution Plate U-bottom\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Generic 2 mL Screwcap\nUSA Scientific 12 Well Reservoir 22 mL #1061-8150\nOpentrons 96 Tip Rack 1000 \u00b5L\nAgilent 1 Well Reservoir 290 mL #201252-100\n", "markdown": { - "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n\n", + "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* MACHEREY-NAGEL NucleoMag\u00ae Tissue\n\n\n", "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/deck.png)\n\n\n", "description": "![MACHEREY-NAGEL](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/MN_Logo_50.jpeg)\n\nThis protocol automates the NucleoMag\u00ae Tissue kit for flexible magnetic bead based isolation.\n\nBefore beginning the protocol on the OT-2, the following preparation steps are needed.\n1. Perform the lysis according to the NucleoMag\u00ae Tissue user manual.\n2. Fill the 12-Well Buffer Reservoir according to the table below.\n3. Resuspend the NucleoMag\u00ae B-Beads by vortexing and place them in Position A1 of the 2mL Tube Rack.\n4. Load the instrument deck according to the displayed positions.\n5. Place the Square-well Block containing the lysates on the Magnetic Module and start the run.\n\n\nYou can access the full description of this workflow on the OT-2 by visiting this link: [link](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel-nucleomag-tissue/thepdf.pdf)\n\n\n", diff --git a/protoBuilds/macherey-nagel-nucleomag-virus/README.json b/protoBuilds/macherey-nagel-nucleomag-virus/README.json index fdcb07c83..5e7167184 100644 --- a/protoBuilds/macherey-nagel-nucleomag-virus/README.json +++ b/protoBuilds/macherey-nagel-nucleomag-virus/README.json @@ -10,7 +10,7 @@ "internal": "macherey-nagel-nucleomag-virus", "labware": "\nMacherey Nagel 96 Well Square Well Block\nMacherey Nagel 96 Well Elution Plate U-bottom\nOpentrons 96 Tip Rack 300 \u00b5L\nOpentrons 24 Tube Rack with Generic 2 mL Screwcap\nUSA Scientific 12 Well Reservoir 22 mL #1061-8150\nOpentrons 96 Tip Rack 1000 \u00b5L\nAgilent 1 Well Reservoir 290 mL #201252-100\n", "markdown": { - "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n\n", + "author": "[MACHEREY-NAGEL](https://www.mn-net.com/us)\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* MACHEREY-NAGEL NucleoMag\u00ae Virus\n\n\n", "deck-setup": "![deck](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/deck.png)\n\n\n", "description": "![MACHEREY-NAGEL](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel/MN_Logo_50.jpeg)\n\nThis protocol automates the NucleoMag\u00ae Virus kit for flexible magnetic bead based isolation.\n\nBefore beginning the protocol on the OT-2, the following preparation steps are needed.\n1. Perform the lysis according to the NucleoMag\u00ae Virus user manual.\n2. Fill the 12-Well Buffer Reservoir according to the table below.\n3. Resuspend the NucleoMag\u00ae V-Beads by vortexing and place them in Position A1 of the 2mL Tube Rack.\n4. Load the instrument deck according to the displayed positions.\n5. Place the Square-well Block containing the lysates on the Magnetic Module and start the run.\n\n\nYou can access the full description of this workflow on the OT-2 by visiting this link: [link](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/macherey-nagel-nucleomag-virus/thepdf.pdf)\n\n\n", diff --git a/protoBuilds/normalization/README.json b/protoBuilds/normalization/README.json index 1d4595079..626f40e79 100644 --- a/protoBuilds/normalization/README.json +++ b/protoBuilds/normalization/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Featured": [ "Normalization" @@ -8,7 +8,7 @@ "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# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/normalization). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Featured\n\t* Normalization\n\n", "description": "![Normalization Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/normalization/normalization_example.png)\n\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\n---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Opentrons Single-Channel Pipette](https://shop.opentrons.com/collections/ot-2-pipettes) and corresponding [Tips](https://shop.opentrons.com/collections/opentrons-tips)\n* [Samples in a compatible plate (96-well or 384-well)](https://labware.opentrons.com/?category=wellPlate)\n* [Automation-friendly reservoir](https://labware.opentrons.com/?category=reservoir)\n* Diluent\n\nFor more detailed information on compatible labware, please visit our [Labware Library](https://labware.opentrons.com/).\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\n**CSV Format**\n\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\n![Normalization CSV](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/normalization/normalization_csv.png)\n\nIn this example, 40\u03bcL will be added to A1, 41\u03bcL will be added to well B1, and so on.\n\nIf you\u2019d like to follow our template, you can make a copy of [this spreadsheet](https://opentrons-protocol-library-website.s3.amazonaws.com/Technical+Notes/normalization/Opentrons+Normalization+Template.xlsx), fill out your values, and export as CSV from there.\n\n*Note 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\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.\n\n\n\n", "internal": "normalization\n", diff --git a/protoBuilds/nucleic_acid_purification_with_magnetic_beads/README.json b/protoBuilds/nucleic_acid_purification_with_magnetic_beads/README.json index 55f84a6ae..d4ae0fc09 100644 --- a/protoBuilds/nucleic_acid_purification_with_magnetic_beads/README.json +++ b/protoBuilds/nucleic_acid_purification_with_magnetic_beads/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons", "categories": { "Featured": [ "Nucleic Acid Purification with Magnetic Beads (Universal)" @@ -8,7 +8,7 @@ "description": "With this protocol, you can perform high-quality nucleic acid purifications using magnetic beads and the Opentrons Magnetic Module. This protocol contains flexible parameters that you can customize for many different magnetic bead and nucleic acid types. Use this setup to rapidly iterate and optimize your magbead-based workflows!\nYou can use any magnetic beads you prefer with this protocol, but we have included some reagent recommendations in the Materials Needed section below to help you get started. For more detailed information on how to use this protocol, please see our Technical Note.\n\n\n\n-- Opentrons OT-2\n-- Opentrons Magnetic Module\n-- Opentrons OT-2 Run App (Version 3.1.2 or later)\n-- 200uL or 300 uL Tiprack (Opentrons tips suggested)\n-- 12-row automation-friendly trough\n-- BioRad HardShell 96-Well PCR Plate\n-- Magnetic Beads (Looking for a kit? We recommend trying Omega Bio-tek Mag-Bind\u00ae TotalPure NGS)\n-- Ethanol\n-- Elution Buffer (Typically 10 mM Tris pH 8.0, TE Buffer, or nuclease-free water)\n\n\n\nUsing the customization fields below, set up your protocol as follows:\n\nPipette: Specify your pipette. We recommend using a p50 or p300 multi- or single-channel.\nPipette Mount: Specify which mount (left or right) your pipette is on.\nSample number: Customize the number of samples to run per protocol. A multiple of 8 is recommended when you are using a multichannel pipette.\nSample volume: Specify the starting volume (in uL) of the input sample.\nBead Ratio: Customize the ratio of beads for left or right side size-selection of fragments. The default bead ratio is 1.8x the input sample volume.\nElution Volume: Specify the final volume (in uL) to elute the purified nucleic acid. The Opentrons MagDeck supports elution volumes above 10 \u00b5L.\nIncubation Time: Specify the amount of time (in minutes) that the bead solution and input sample interact.\nSettling Time: Specify the amount of time (in minutes) needed to pellet the beads. Higher volumes may require a longer settling time.\nDrying Time: Specify the drying time (in minutes) needed after wash steps.\n\n\n", "internal": "Nucleic Acid Purification, v1", "markdown": { - "author": "[Opentrons](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://https://library.opentrons.com/p/nucleic_acid_purification_with_magnetic_beads). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons](https://opentrons.com/)\n\n\n", "categories": "* Featured\n * Nucleic Acid Purification with Magnetic Beads (Universal)\n\n", "description": "With this protocol, you can perform high-quality nucleic acid purifications using magnetic beads and the [Opentrons Magnetic Module](https://shop.opentrons.com/products/magdeck]). This protocol contains flexible parameters that you can customize for many different magnetic bead and nucleic acid types. Use this setup to rapidly iterate and optimize your magbead-based workflows!\n\nYou can use any magnetic beads you prefer with this protocol, but we have included some reagent recommendations in the **Materials Needed** section below to help you get started. For more detailed information on how to use this protocol, please see our [Technical Note](https://s3.amazonaws.com/opentrons-protocol-library-website/Technical+Notes/Nucleic+Acid+Purification+with+Magnetic+Module+OT2+Technical+Note.pdf).\n\n---\n\n---\n\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/customizable-serial-dilution/materials.png)\n\n-- [Opentrons OT-2](http://opentrons.com/ot-2)\n\n-- [Opentrons Magnetic Module](https://shop.opentrons.com/products/magdeck?_ga=2.171718441.823190023.1542396855-403439593.1535387376)\n\n-- [Opentrons OT-2 Run App (Version 3.1.2 or later)](http://opentrons.com/ot-app)\n\n-- 200uL or 300 uL Tiprack ([Opentrons tips suggested](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips-racks-9-600-tips))\n\n-- [12-row automation-friendly trough](https://www.usascientific.com/12-channel-automation-reservoir.aspx)\n\n-- [BioRad HardShell 96-Well PCR Plate](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\n-- Magnetic Beads (Looking for a kit? We recommend trying [Omega Bio-tek Mag-Bind\u00ae TotalPure NGS](https://shop.opentrons.com/products/mag-bind-total-pure-ngs))\n\n-- Ethanol\n\n-- Elution Buffer (Typically 10 mM Tris pH 8.0, TE Buffer, or nuclease-free water)\n\n---\n\n---\n\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\nUsing the customization fields below, set up your protocol as follows:\n\n * **Pipette:** Specify your pipette. We recommend using a p50 or p300 multi- or single-channel.\n * **Pipette Mount:** Specify which mount (left or right) your pipette is on.\n * **Sample number:** Customize the number of samples to run per protocol. A multiple of 8 is recommended when you are using a multichannel pipette.\n * **Sample volume:** Specify the starting volume (in uL) of the input sample.\n * **Bead Ratio:** Customize the ratio of beads for left or right side size-selection of fragments. *The default bead ratio is 1.8x the input sample volume.*\n * **Elution Volume:** Specify the final volume (in uL) to elute the purified nucleic acid. *The Opentrons MagDeck supports elution volumes above 10 \u00b5L.*\n * **Incubation Time:** Specify the amount of time (in minutes) that the bead solution and input sample interact.\n * **Settling Time:** Specify the amount of time (in minutes) needed to pellet the beads. *Higher volumes may require a longer settling time.*\n * **Drying Time:** Specify the drying time (in minutes) needed after wash steps.\n\n---\n\n---\n\n", "internal": "Nucleic Acid Purification, v1\n\n", diff --git a/protoBuilds/omega_biotek_magbind_totalpure_NGS/README.json b/protoBuilds/omega_biotek_magbind_totalpure_NGS/README.json index f1c35081f..255379496 100644 --- a/protoBuilds/omega_biotek_magbind_totalpure_NGS/README.json +++ b/protoBuilds/omega_biotek_magbind_totalpure_NGS/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)", + "author": "Opentrons (verified)\nOmega Bio-tek\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", "categories": { "Featured": [ "NGS Cleanup and Size Selection with Omega Bio-tek Mag-Bind\u00ae TotalPure" @@ -8,18 +8,16 @@ "description": "\nWith this protocol, you can perform high-quality nucleic acid purifications using Omega Bio-tek Mag-Bind\u00ae TotalPure NGS magnetic beads and the Opentrons Magnetic Module. This setup yields high quality PCR product and other nucleic acids without the use of centrifugation or vacuum separation.\nThis kit is widely used in NGS cleanup for its affordability and simplicity. It is also well-adapted for nucleic acid size selection by varying bead ratios for the isolation of a wide array of fragment sizes. For more detailed information on how to use this protocol, please see our Application Note.\nPlease note this protocol is currently being updated.\n\n\n\nTo purchase tips, reagents, or our Magnetic Module, please visit our online store or contact our Sales team at info@opentrons.com.\n\nOmega Bio-tek Mag-Bind\u00ae TotalPure NGS Kit\nOpentrons OT-2\nOpentrons Magnetic Module\nOpentrons OT-2 Run App (Version 3.1.2 or later)\n200uL or 300 uL Tiprack (Opentrons tips suggested)\n12-row automation-friendly trough\nBioRad HardShell 96-Well PCR Plates\nEthanol\nElution Buffer (Typically 10 mM Tris pH 8.0, TE Buffer, or nuclease-free water)\n\n\n\n\nUsing the customization fields below, set up your protocol as follows:\n\nPipette: Specify your pipette. We recommend using a p50 or p300 multi- or single-channel.\nPipette Mount: Specify which mount (left or right) your pipette is on.\nSample number: Customize the number of samples to run per protocol. A multiple of 8 is recommended when you are using a multichannel pipette.\nSample volume: Specify the starting volume (in uL) of the input sample.\nBead Ratio: Customize the ratio of beads for left or right side size-selection of fragments. The default bead ratio is 1.8x the input sample volume.\nElution Volume: Specify the final volume (in uL) to elute the purified nucleic acid. The Opentrons MagDeck supports elution volumes above 10 \u00b5L.\n\nMake sure to add reagents to your labware before placing it on the deck! You can see where to place your reagents below.\n\n\n", "internal": "Omega Nucleic Acid Purification, v2", "markdown": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n[Omega Bio-tek](http://omegabiotek.com/store/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/omega_biotek_magbind_totalpure_ngs). This page won\u2019t be available after March 31st, 2024.\n\n", "categories": "* Featured\n * NGS Cleanup and Size Selection with Omega Bio-tek Mag-Bind\u00ae TotalPure\n\n", "description": "![Omega Bio-tek](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Omega+Logo.png)\n\nWith this protocol, you can perform high-quality nucleic acid purifications using [Omega Bio-tek Mag-Bind\u00ae TotalPure NGS](https://shop.opentrons.com/products/mag-bind-total-pure-ngs) magnetic beads and the [Opentrons Magnetic Module](https://shop.opentrons.com/products/magdeck). This setup yields high quality PCR product and other nucleic acids without the use of centrifugation or vacuum separation.\n\nThis kit is widely used in NGS cleanup for its affordability and simplicity. It is also well-adapted for nucleic acid size selection by varying bead ratios for the isolation of a wide array of fragment sizes. For more detailed information on how to use this protocol, please see our [Application Note](https://s3.amazonaws.com/opentrons-protocol-library-website/Technical+Notes/Omega_Application_Note.pdf).\n\nPlease note this protocol is currently being updated.\n\n---\n\n---\n\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase tips, reagents, or our Magnetic Module, please [visit our online store](https://shop.opentrons.com/) or contact our Sales team at .\n\n * [Omega Bio-tek Mag-Bind\u00ae TotalPure NGS Kit](https://shop.opentrons.com/products/mag-bind-total-pure-ngs)\n * [Opentrons OT-2](http://opentrons.com/ot-2)\n * [Opentrons Magnetic Module](https://shop.opentrons.com/products/magdeck)\n * [Opentrons OT-2 Run App (Version 3.1.2 or later)](http://opentrons.com/ot-app)\n * 200uL or 300 uL Tiprack ([Opentrons tips suggested](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-300ul-tips-racks-9-600-tips))\n * [12-row automation-friendly trough](https://shop.opentrons.com/collections/verified-labware/products/nest-12-well-reservoir-15-ml)\n * [BioRad HardShell 96-Well PCR Plates](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 * Ethanol\n * Elution Buffer (Typically 10 mM Tris pH 8.0, TE Buffer, or nuclease-free water)\n\n---\n\n---\n\n\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\nUsing the customization fields below, set up your protocol as follows:\n\n * **Pipette:** Specify your pipette. We recommend using a p50 or p300 multi- or single-channel.\n * **Pipette Mount:** Specify which mount (left or right) your pipette is on.\n * **Sample number:** Customize the number of samples to run per protocol. A multiple of 8 is recommended when you are using a multichannel pipette.\n * **Sample volume:** Specify the starting volume (in uL) of the input sample.\n * **Bead Ratio:** Customize the ratio of beads for left or right side size-selection of fragments. *The default bead ratio is 1.8x the input sample volume.*\n * **Elution Volume:** Specify the final volume (in uL) to elute the purified nucleic acid. *The Opentrons MagDeck supports elution volumes above 10 \u00b5L.*\n\nMake sure to add reagents to your labware before placing it on the deck! You can see where to place your reagents below.\n\n![Labware setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/Nucleic+Acid+Purification/Nucleic+Acid+Purification+with+Magnetic+Beads+-+Reagent+Start+Position.png)\n\n---\n\n---\n\n", "internal": "Omega Nucleic Acid Purification, v2\n\n", "notes": "Please reference our [Application Note](https://s3.amazonaws.com/opentrons-protocol-library-website/Technical+Notes/Omega_Application_Note.pdf) for more information about the expected output of this protocol, in addition to expanded sample data from the Opentrons and Omega Bio-tek labs.\n\nIf you'd like to request a more complex purification workflow, please use our [Protocol Development Request Form](https://opentrons-protocol-dev.paperform.co/). You can also download the Python file from this page and modify it using our [API Documentation](https://docs.opentrons.com/). For additional questions about this protocol, please email .\n\nIf you are interested in purchasing the Opentrons Magnetic Module or trying out the Omega Bio-tek Mag-Bind\u00ae beads, please contact our Sales Team at to learn more!\n\n", - "partner": "[Omega Bio-tek](http://omegabiotek.com/store/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/omega_biotek_magbind_totalpure_ngs). This page won\u2019t be available after March 31st, 2024.\n\n", "preview": "With this protocol, you can perform high-quality nucleic acid purifications using the [Opentrons Magnetic Module](https://shop.opentrons.com/products/magdeck) and [Omega Bio-tek Mag-Bind\u00ae TotalPure NGS](https://shop.opentrons.com/products/mag-bind-total-pure-ngs) magnetic beads. This kit is widely used in NGS cleanup for its affordability and simplicity. You can select specific sizes of nucleic acids by varying the bead-to-DNA ratio across a wide array of fragment sizes. For reagent and module purchasing details contact .\n", "process": "1. Select all desired settings according to the \"Setup\" section above to create your customized protocol.\n2. Download your customized OT-2 protocol using the blue \"Download\" button.\n3. Upload your protocol file into the Opentrons Run App and follow the instructions there to set up your deck and proceed to run!\n4. Make sure to add reagents to your labware before placing it on the deck! You can see where to place your reagents in the \"Setup\" section above.\n\n", "title": "NGS Cleanup and Size Selection with Omega Bio-tek Mag-Bind\u00ae TotalPure NGS" }, "notes": "Please reference our Application Note for more information about the expected output of this protocol, in addition to expanded sample data from the Opentrons and Omega Bio-tek labs.\nIf you'd like to request a more complex purification workflow, please use our Protocol Development Request Form. You can also download the Python file from this page and modify it using our API Documentation. For additional questions about this protocol, please email protocols@opentrons.com.\nIf you are interested in purchasing the Opentrons Magnetic Module or trying out the Omega Bio-tek Mag-Bind\u00ae beads, please contact our Sales Team at info@opentrons.com to learn more!", - "partner": "Omega Bio-tek\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", "preview": "With this protocol, you can perform high-quality nucleic acid purifications using the Opentrons Magnetic Module and Omega Bio-tek Mag-Bind\u00ae TotalPure NGS magnetic beads. This kit is widely used in NGS cleanup for its affordability and simplicity. You can select specific sizes of nucleic acids by varying the bead-to-DNA ratio across a wide array of fragment sizes. For reagent and module purchasing details contact info@opentrons.com.", "process": "\nSelect all desired settings according to the \"Setup\" section above to create your customized protocol.\nDownload your customized OT-2 protocol using the blue \"Download\" button.\nUpload your protocol file into the Opentrons Run App and follow the instructions there to set up your deck and proceed to run!\nMake sure to add reagents to your labware before placing it on the deck! You can see where to place your reagents in the \"Setup\" section above.\n", "title": "NGS Cleanup and Size Selection with Omega Bio-tek Mag-Bind\u00ae TotalPure NGS" diff --git a/protoBuilds/pcr_prep_part_1/README.json b/protoBuilds/pcr_prep_part_1/README.json index 05a04b7be..9668d9290 100644 --- a/protoBuilds/pcr_prep_part_1/README.json +++ b/protoBuilds/pcr_prep_part_1/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "PCR": [ "Mastermix Assembly" @@ -10,7 +10,7 @@ "internal": "OT-2 PCR Prep v2", "labware": "\n4-in-1 Tube Rack Set\n12-well Trough\n", "markdown": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/pcr_prep_part_1). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* PCR\n * Mastermix Assembly\n\n", "deck-setup": "* Slot 1: Option of Opentrons tuberack/tube combo 1, or none\n* Slot 2: Option of Opentrons tuberack/tube combo 2, or none\n* Slot 3: Choice of Opentrons labware library 12-well reservoir\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/pcr_prep_part_1/deck.jpg)\n\n", "description": "Part 1 of 2: Master Mix Assembly\n\nLinks:\n* [Part 1: Master Mix Assembly](./pcr_prep_part_1)\n* [Part 2: Master Mix Distribution and DNA Transfer](./pcr_prep_part_2)\n\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.\n\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\n---\n\n", diff --git a/protoBuilds/pcr_prep_part_2/README.json b/protoBuilds/pcr_prep_part_2/README.json index d53e59455..8a369ef37 100644 --- a/protoBuilds/pcr_prep_part_2/README.json +++ b/protoBuilds/pcr_prep_part_2/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "PCR": [ "PCR Prep" @@ -8,7 +8,7 @@ "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# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/pcr_prep_part_2). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* PCR\n * PCR Prep\n\n", "description": "Part 2 of 2: Master Mix Distribution and DNA Transfer\n\nLinks:\n* [Part 1: Master Mix Assembly](./pcr_prep_part_1)\n* [Part 2: Master Mix Distribution and DNA Transfer](./pcr_prep_part_2)\n\n\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\n---\n\nYou will need:\n* [12-channel reservoir](https://www.usascientific.com/12-channel-automation-reservoir.aspx)\n* [96-well PCR plate](https://www.bio-rad.com/en-us/sku/hsp9601-hard-shell-96-well-pcr-plates-low-profile-thin-wall-skirted-white-clear?ID=hsp9601)\n\n", "internal": "OT-2 PCR Prep v2\n", diff --git a/protoBuilds/sci-macherey-nagel-nucleomag/README.json b/protoBuilds/sci-macherey-nagel-nucleomag/README.json index e3be31214..cbffe48e3 100644 --- a/protoBuilds/sci-macherey-nagel-nucleomag/README.json +++ b/protoBuilds/sci-macherey-nagel-nucleomag/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "Nucleic Acid Extraction & Purification": [ "DNA Extraction" @@ -10,7 +10,7 @@ "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": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-macherey-nagel-nucleomag). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* DNA Extraction\n\n", "deck-setup": "\n* Tip rack on Slot 4 is used for tip parking if selected.\n\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-macherey-nagel-nucleomag/nucleomag-virus-isolation.png)\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\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-macherey-nagel-nucleomag/NucleoMag+Virus+Viral+DNA%3ARNA+Isolation-results.png)\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\n---\n\n", diff --git a/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json b/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json index d979fa92e..6b0fc112f 100644 --- a/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json +++ b/protoBuilds/sci-mag-bind-blood-tissue-kit/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "Nucleic Acid Extraction & Purification": [ "DNA Extraction" @@ -10,7 +10,7 @@ "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": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-mag-bind-blood-tissue-kit). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* DNA Extraction\n\n", "deck-setup": "\n* Tip rack on Slot 4 is used for tip parking if selected.\n\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit.png)\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\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-mag-bind-blood-tissue-kit/sci-mag-bind-blood-tissue-kit-results.png)\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\n---\n\n", diff --git a/protoBuilds/sci-omegabiotek-extraction-fa/README.json b/protoBuilds/sci-omegabiotek-extraction-fa/README.json index dbe1c6ee7..3bab2d055 100644 --- a/protoBuilds/sci-omegabiotek-extraction-fa/README.json +++ b/protoBuilds/sci-omegabiotek-extraction-fa/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "Nucleic Acid Extraction & Purification": [ "RNA Extraction" @@ -10,7 +10,7 @@ "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": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-omegabiotek-extraction-fa). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* RNA Extraction\n\n", "deck-setup": "\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-omegabiotek-extraction/Screen+Shot+2021-06-29+at+5.29.44+PM.png)\n\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.\n\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-omegabiotek-extraction/Screen+Shot+2021-06-29+at+2.44.45+PM.png)\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\n\n---\n\n", diff --git a/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json b/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json index 97554d94d..2ba61b040 100644 --- a/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json +++ b/protoBuilds/sci-omegabiotek-magbind-total-rna-96/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "Nucleic Acid Extraction & Purification": [ "RNA Extraction" @@ -10,7 +10,7 @@ "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": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-omegabiotek-magbind-total-rna-96). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* RNA Extraction\n\n", "deck-setup": "\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/528c16/Screen+Shot+2022-03-11+at+3.25.12+PM.png)\n\nSaliva: add 200uL of saliva\n\nBacteria culture: spin down 200uL of culture, wash once in PBS, resuspend in 200uL of chilled PBS\n\n200uL of sample + 200uL of lysis buffer. Mix thoroughly, add to deep well plate\n\nDnase 1 treatment: 49uL of buffer + 1uL of DNAse 1 per sample.\n![reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/528c16/Screen+Shot+2022-03-11+at+3.25.34+PM.png)\n\n![reagent volumes](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/528c16/Screen+Shot+2022-03-11+at+3.26.29+PM.png)\n\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](https://www.omegabiotek.com/product/mag-bind-total-rna-96-kit/):\n\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.\"\n\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-omegabiotek-magbind-total-rna-96/Screen+Shot+2021-08-09+at+4.10.56+PM.png)\n\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-omegabiotek-magbind-total-rna-96/Screen+Shot+2021-08-09+at+4.11.10+PM.png)\n\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\n\n---\n\n", diff --git a/protoBuilds/sci-omegabiotek-magbind/README.json b/protoBuilds/sci-omegabiotek-magbind/README.json index 42b567b0e..02607a95f 100644 --- a/protoBuilds/sci-omegabiotek-magbind/README.json +++ b/protoBuilds/sci-omegabiotek-magbind/README.json @@ -10,7 +10,7 @@ "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": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-omegabiotek-magbind). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-omegabiotek-magbind). This page won\u2019t be available after March 31st, 2024.\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* RNA Extraction\n\n", "deck-setup": "Tip rack on Slot 5 is used for tip parking if selected. If not tip parking, place [200ul Opentrons Filter Tip Rack](https://shop.opentrons.com/collections/opentrons-tips/products/opentrons-200ul-filter-tips) in Slot 5.\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-omegabiotek-magbind/Screen+Shot+2021-08-09+at+11.44.26+AM.png)\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]((https://www.omegabiotek.com/product/mag-bind-viral-dna-rna-96-kit/):\n\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.\"\n\nResults of the Opentrons Science team's internal testing of this protocol on the OT-2 are shown below: \n\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-omegabiotek-magbind/Screen+Shot+2021-08-09+at+11.16.53+AM.png)\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\n\n---\n\n", 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 73cdf2545..fb192cc3e 100644 --- a/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/README.json +++ b/protoBuilds/sci-promega-magazorb-dna-mini-prep-kit/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "Nucleic Acid Extraction & Purification": [ "DNA Extraction" @@ -10,7 +10,7 @@ "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": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-promega-magazorb-dna-mini-prep-kit). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* DNA Extraction\n\n", "deck-setup": "\n* Tip rack on Slot 4 is used for tip parking if selected.\n\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-promega-magazorb-dna-mini-prep-kit/promega-extraction-layout.png)\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\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-promega-magazorb-dna-mini-prep-kit/promega-magazordb-results.png)\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\n\n---\n\n", diff --git a/protoBuilds/sci-zymo-directzol-magbead/README.json b/protoBuilds/sci-zymo-directzol-magbead/README.json index b60ef40e6..f807f84a2 100644 --- a/protoBuilds/sci-zymo-directzol-magbead/README.json +++ b/protoBuilds/sci-zymo-directzol-magbead/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", + "author": "Opentrons (verified)", "categories": { "Nucleic Acid Extraction & Purification": [ "RNA Extraction" @@ -10,7 +10,7 @@ "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": { - "author": "[Opentrons (verified)](https://opentrons.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-zymo-directzol-magbead). This page won\u2019t be available after March 31st, 2024.\n\n", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n\n", "categories": "* Nucleic Acid Extraction & Purification\n\t* RNA Extraction\n\n", "deck-setup": "\n* Tip rack on Slot 4 is used for tip parking if selected.\n\n![deck layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-zymo-directzol-magbead/Screen+Shot+2021-07-27+at+11.06.38+AM.png)\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![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-zymo-directzol-magbead/Screen+Shot+2021-07-27+at+11.12.53+AM.png)\n\n![results](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/sci-zymo-directzol-magbead/Screen+Shot+2021-07-27+at+11.13.04+AM.png)\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\n\n---\n\n", diff --git a/protoBuilds/swift-2s-turbo-pt1/README.json b/protoBuilds/swift-2s-turbo-pt1/README.json index d285d4b6f..7dd5e4542 100644 --- a/protoBuilds/swift-2s-turbo-pt1/README.json +++ b/protoBuilds/swift-2s-turbo-pt1/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)", + "author": "Opentrons (verified)\nSwift Biosciences\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", "categories": { "Featured": [ "NGS Library Prep: Swift 2S Turbo" @@ -8,18 +8,16 @@ "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", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n[Swift Biosciences](https://swiftbiosci.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/swift-2s-turbo-pt1). This page won\u2019t be available after March 31st, 2024.\n\n", "categories": "* Featured\n\t* NGS Library Prep: Swift 2S Turbo\n\n\n", "description": "![Swift Biosciences](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/swift-2s-protocol/swift_logo.jpg)\n\nPart 1 of 3: Enzymatic Prep & Ligation\n\n\nWith this protocol, your [OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2) can perform the [Swift 2S Turbo DNA Library Kit](https://swiftbiosci.com/swift-2s-turbo-dna-library-kits/). For more information about the Swift 2S Turbo Kit and the [Swift 2S Turbo Unique Dual Indexing Primer Kit](https://shop.opentrons.com/products/swift-2s-turbo-unique-dual-indexing-primer-kit-96-rxns?_pos=1&_sid=f1fb599e7&_ss=r) 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](https://opentrons-landing-img.s3.amazonaws.com/bundles/swift_automated_ngs_application_note.pdf)\n\n\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](https://swiftbiosci.com/wp-content/uploads/2019/11/PRT-001-2S-Turbo-DNA-Library-Kit-Rev-1.pdf).\n\n\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](https://protocols.opentrons.com/protocol/swift-2s-turbo-pt2).\n\n\nLinks:\n* [Part 1: Enzymatic Prep & Ligation](https://protocols.opentrons.com/protocol/swift-2s-turbo-pt1)\n* [Part 2: Ligation Clean-Up & PCR Prep](https://protocols.opentrons.com/protocol/swift-2s-turbo-pt2)\n* [Part 3: Final Clean-Up](https://protocols.opentrons.com/protocol/swift-2s-turbo-pt3)\n\n\n\n**Note:** 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.](https://swiftbiosci.com/wp-content/uploads/2019/12/PRT-022-Swift-Deceleration-Module-Rev-1.pdf)\n\n---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase consumables, labware, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n\n**Attention**: You can now purchase all of the consumables needed to run this protocol by [clicking here](https://shop.opentrons.com/products/ngs-library-prep-workstation-consumables-refill).\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Swift 2S Turbo DNA Library Kit](https://swiftbiosci.com/swift-2s-turbo-dna-library-kits/)\n* [Swift 2S Turbo Unique Dual Indexing Primer Kit](https://shop.opentrons.com/products/swift-2s-turbo-unique-dual-indexing-primer-kit-96-rxns?_pos=1&_sid=f1fb599e7&_ss=r)\n* [Omega Mag-Bind TotalPure NGS Kit](https://shop.opentrons.com/collections/verified-reagents/products/mag-bind-total-pure-ngs)\n* [Opentrons Temperature Module with Aluminum Block Set](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n* [Opentrons Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n* [Opentrons P20 Single-Channel Pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette) or Opentrons P50 Single-Channel Pipette*\n* [Opentrons P300 Multi-Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n* [Opentrons Tips](https://shop.opentrons.com/collections/opentrons-tips)\n* [NEST 96-Well PCR Plate](https://shop.opentrons.com/collections/lab-plates/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [NEST 12-Well Reservoir, 15mL](https://shop.opentrons.com/collections/reservoirs/products/nest-12-well-reservoir-15-ml)\n* [NEST 2mL Tubes](https://shop.opentrons.com/collections/tubes/products/nest-2-0-ml-sample-vial)\n* Samples, resuspended in Low EDTA TE, bringing the total volume to 16\u00b5L\n* PCR Strip(s), *optional*\n\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.\n\n\nFull setup for the entire protocol:\n\n![Full Deck Layout](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/swift-2s-protocol/deck_layout_names.png)\n\n![Layout of Reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/swift-2s-protocol/labware_layout.jpeg)\n\n\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\n\n*Specific to Part 1 of 3*\n\n\nSlot 1: [NEST 96-Well PCR Plate](https://shop.opentrons.com/collections/lab-plates/products/nest-0-1-ml-96-well-pcr-plate-full-skirt) (or PCR Strips) on top of [96-Well Aluminum Block](https://shop.opentrons.com/collections/racks-and-adapters/products/aluminum-block-set) with samples\n* 8 Samples: Column 1\n* 16 Samples: Columns 1 & 2\n* 24 Samples: Columns 1, 2, & 3\n\nSlot 3: [Opentrons Temperature Module with 24-Well Aluminum Block](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck) and [NEST 2mL Tubes](https://shop.opentrons.com/collections/tubes/products/nest-2-0-ml-sample-vial) with master mixes (for more information on master mixes, [click here](https://opentrons-protocol-library-website.s3.amazonaws.com/Technical+Notes/swift-2s-turbo-pt1/Swift+2S+Turbo+Master+Mix+Volumes.xlsx))\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...)\n\n\nSlot 5: [Opentrons Tips](https://shop.opentrons.com/collections/opentrons-tips)\n\n\n\n\n__Using 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.\n\n\n\n\n", "internal": "Swift-2S-Turbo-pt1\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", - "partner": "[Swift Biosciences](https://swiftbiosci.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/swift-2s-turbo-pt1). This page won\u2019t be available after March 31st, 2024.\n\n", "process": "\n1. Input your protocol parameters.\n2. Download your protocol.\n3. Upload your protocol into the [OT App](https://opentrons.com/ot-app).\n4. Set up your deck according to the deck map.\n5. 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).\n6. Hit \"Run\".\n\n", "robot": "* [OT-2](https://opentrons.com/ot-2)\n\n", "title": "Swift 2S Turbo DNA Library Kit Protocol: Part 1/3 - Enzymatic Prep & Ligation" }, "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Swift Biosciences\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", "process": "\nInput your protocol parameters.\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 articles.\nHit \"Run\".\n", "robot": [ "OT-2" diff --git a/protoBuilds/swift-fully-automated/README.json b/protoBuilds/swift-fully-automated/README.json index e7a41c291..08f9e1b5b 100644 --- a/protoBuilds/swift-fully-automated/README.json +++ b/protoBuilds/swift-fully-automated/README.json @@ -1,5 +1,5 @@ { - "author": "Opentrons (verified)", + "author": "Opentrons (verified)\nSwift Biosciences\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", "categories": { "NGS Library Prep": [ "Swift 2S Turbo" @@ -8,18 +8,16 @@ "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", + "author": "[Opentrons (verified)](https://opentrons.com/)\n\n[Swift Biosciences](https://swiftbiosci.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/swift-fully-automated). This page won\u2019t be available after March 31st, 2024.\n\n", "categories": "* NGS Library Prep\n\t* Swift 2S Turbo\n\n\n", "description": "![Swift Biosciences](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/swift-2s-protocol/swift_logo.jpg)\n\n\nWith this protocol, your [OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2) can **fully automate** the entire [Swift 2S Turbo DNA Library Kit](https://swiftbiosci.com/swift-2s-turbo-dna-library-kits/). 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.\n\n\nFor more information about the Swift 2S Turbo Kit and the [Swift 2S Turbo Unique Dual Indexing Primer Kit](https://shop.opentrons.com/products/swift-2s-turbo-unique-dual-indexing-primer-kit-96-rxns?_pos=1&_sid=f1fb599e7&_ss=r) 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](https://opentrons-landing-img.s3.amazonaws.com/bundles/swift_automated_ngs_application_note.pdf)
\n
\n**Update (April 12, 2021)**: This protocol has been updated to fix an issue with the final elution destination when selecting 16 samples.
\n**Update (April 13, 2021)**: This protocol has been updated to accommodate the GEN2 Magnetic Module and fix an issue when using 200\u00b5L filter tips.
\n**Update (September 2, 2021)**: This protocol has been updated to allow for the [GEN2 P300 8-Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-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\n---\n![Materials Needed](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/materials.png)\n\nTo purchase consumables, labware, or pipettes, please visit our [online store](https://shop.opentrons.com/) or contact our sales team at [info@opentrons.com](mailto:info@opentrons.com)\n\n\n**Attention**: You can now purchase all of the consumables needed to run this protocol by [clicking here](https://shop.opentrons.com/products/ngs-library-prep-workstation-consumables-refill).\n\n* [Opentrons OT-2](https://shop.opentrons.com/collections/ot-2-robot/products/ot-2)\n* [Opentrons OT-2 Run App (Version 3.15.0 or later)](https://opentrons.com/ot-app/)\n* [Swift 2S Turbo DNA Library Kit](https://swiftbiosci.com/swift-2s-turbo-dna-library-kits/)\n* [Swift 2S Turbo Unique Dual Indexing Primer Kit](https://shop.opentrons.com/products/swift-2s-turbo-unique-dual-indexing-primer-kit-96-rxns?_pos=1&_sid=f1fb599e7&_ss=r)\n* [Omega Mag-Bind TotalPure NGS Kit](https://shop.opentrons.com/collections/verified-reagents/products/mag-bind-total-pure-ngs)\n* [Opentrons Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module)\n* [Opentrons Temperature Module with Aluminum Block Set](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck)\n* [Opentrons Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n* [Opentrons P20 Single-Channel Pipette](https://shop.opentrons.com/collections/ot-2-pipettes/products/single-channel-electronic-pipette) or Opentrons P50 Single-Channel Pipette*\n* [Opentrons P300 Multi-Channel Pipette](https://shop.opentrons.com/collections/ot-2-robot/products/8-channel-electronic-pipette)\n* [Opentrons Tips](https://shop.opentrons.com/collections/opentrons-tips)\n* [NEST 96-Well PCR Plate](https://shop.opentrons.com/collections/lab-plates/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* [NEST 12-Well Reservoir, 15mL](https://shop.opentrons.com/collections/reservoirs/products/nest-12-well-reservoir-15-ml)\n* [NEST 2mL Tubes](https://shop.opentrons.com/collections/tubes/products/nest-2-0-ml-sample-vial)\n* Samples, resuspended in Low EDTA TE, bringing the total volume to 19.5\u00b5L\n\n\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.\n\n\nFull setup for the entire protocol:\n\n![Full Deck Layout](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/swift-2s-protocol/swift-fa-layout.png)\n\n![Layout of Reagents](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/swift-2s-protocol/swift-fa-labware.jpeg)\n\n\n\n\n---\n![Setup](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/001-General+Headings/Setup.png)\n\n\nSlot 1: [NEST 96-Well PCR Plate](https://shop.opentrons.com/collections/lab-plates/products/nest-0-1-ml-96-well-pcr-plate-full-skirt) on [Opentrons Magnetic Module](https://shop.opentrons.com/collections/hardware-modules/products/magdeck)\n\n\nSlot 2: [NEST 12-Well Reservoir](https://shop.opentrons.com/collections/reservoirs/products/nest-12-well-reservoir-15-ml) 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\n\n\nSlot 3: [Opentrons Temperature Module with 24-Well Aluminum Block](https://shop.opentrons.com/collections/hardware-modules/products/tempdeck) and [NEST 2mL Tubes](https://shop.opentrons.com/collections/tubes/products/nest-2-0-ml-sample-vial) with master mixes (for more information on master mixes, [click here](https://opentrons-protocol-library-website.s3.amazonaws.com/Technical+Notes/swift-fully-automated/Swift+2s+Turbo+Fully+Automated+MasterMix+Volumes.xlsx)) 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...)\n\n\nSlot 4: [Opentrons Tips for Single-Channel Pipette](https://shop.opentrons.com/collections/opentrons-tips)\n\n\nSlot 5: [Opentrons Tips for P300 8-Channel Pipette](https://shop.opentrons.com/collections/opentrons-tips)\n\n\nSlot 6: [Opentrons Tips for P300 8-Channel Pipette](https://shop.opentrons.com/collections/opentrons-tips)\n\n\nSlot 9: [Opentrons Tips for P300 8-Channel Pipette](https://shop.opentrons.com/collections/opentrons-tips)\n\n\n\nSlot 7/8/10/11: [Opentrons Thermocycler Module](https://shop.opentrons.com/collections/hardware-modules/products/thermocycler-module) with samples in a [NEST 96-Well PCR Plate](https://shop.opentrons.com/collections/lab-plates/products/nest-0-1-ml-96-well-pcr-plate-full-skirt)\n* 8 Samples: Column 1\n* 16 Samples: Columns 1 & 2\n\n\n\n__Using 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](https://opentrons-protocol-library-website.s3.amazonaws.com/Technical+Notes/swift-fully-automated/Swift+Fully+Automated+-+PCR+Cycles+Recommendation.xlsx). 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.\n\n\n\n**Note**: 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\n\n", "internal": "swift-fully-automated\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", - "partner": "[Swift Biosciences](https://swiftbiosci.com/)\n\n# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/swift-fully-automated). This page won\u2019t be available after March 31st, 2024.\n\n", "process": "\n1. Input your protocol parameters.\n2. Download your protocol.\n3. Upload your protocol into the [OT App](https://opentrons.com/ot-app).\n4. Set up your deck according to the deck map.\n5. 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).\n6. Hit \"Run\".\n\n", "robot": "* [OT-2](https://opentrons.com/ot-2)\n\n", "title": "Swift 2S Turbo DNA Library Kit Protocol: Fully Automated" }, "notes": "If you have any questions about this protocol, please contact the Protocol Development Team by filling out the Troubleshooting Survey.", - "partner": "Swift Biosciences\nOpentrons has launched a new Protocol Library. You should use the new page for this protocol. This page won\u2019t be available after March 31st, 2024.", "process": "\nInput your protocol parameters.\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 articles.\nHit \"Run\".\n", "robot": [ "OT-2" diff --git a/protocols/274d2a/README.md b/protocols/274d2a/README.md index d24bf119f..becfead57 100644 --- a/protocols/274d2a/README.md +++ b/protocols/274d2a/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/274d2a). This page won’t be available after March 31st, 2024. ## Categories * Sample Prep diff --git a/protocols/3359a5/README.md b/protocols/3359a5/README.md index d6aca0867..aecac0b29 100644 --- a/protocols/3359a5/README.md +++ b/protocols/3359a5/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/3359a5). This page won’t be available after March 31st, 2024. ## Categories * Featured diff --git a/protocols/6d901d-2/6d901d-2.ot2.apiv2.py b/protocols/6d901d-2/6d901d-2.ot2.apiv2.py index d61152cc8..6833d86ca 100644 --- a/protocols/6d901d-2/6d901d-2.ot2.apiv2.py +++ b/protocols/6d901d-2/6d901d-2.ot2.apiv2.py @@ -1,5 +1,6 @@ from opentrons import protocol_api from opentrons.protocol_api.labware import OutOfTipsError +from opentrons.types import Mount metadata = { @@ -52,7 +53,7 @@ def run(ctx: protocol_api.ProtocolContext): # Parse csv # Format: Source Well, Source Aspiration Height Above Bottom (in mm), - # Dest Well, Volume (in ul) + # Dest Well, Vol (in ul) transfer_info = [[val.strip().lower() for val in line.split(',')] for line in transfer_csv.splitlines() if line.split(',')[0].strip()][1:] @@ -83,11 +84,19 @@ def run(ctx: protocol_api.ProtocolContext): # load pipette pip = ctx.load_instrument(pipette_type, pipette_mount, tip_racks=tipracks) - if 'p20' in pipette_type: - pick_up_current = 0.15 - ctx._hw_manager.hardware._attached_instruments[ - pip._implementation.get_mount()].update_config_item( - 'pick_up_current', pick_up_current) + if not ctx.is_simulating(): + pick_up_current = 0.1 # 100 mA for single tip + # Uncomment the next two lines if using Opentrons Robot Software version 7.1.x. # noqa: E501 + # Comment them if NOT using 7.1.x + + ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pip.mount)).update_config_item( # noqa: E501 + {'pick_up_current': {8: pick_up_current}}) + + # Uncomment the next two lines if using Opentrons Robot Software version 7.2.x # noqa: E501 + # Comment them if NOT using 7.2.x + + # ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pip.mount)).update_config_item( + # {'pick_up_current': pick_up_current}) # Tip_map has the columns reversed, pipette always picks up the # bottom-most tip in a given column until the column is depleted, and then diff --git a/protocols/6d901d-2/README.md b/protocols/6d901d-2/README.md index ff6779c8b..b03c561a8 100644 --- a/protocols/6d901d-2/README.md +++ b/protocols/6d901d-2/README.md @@ -18,7 +18,7 @@ A protocol based on our most robust [cherrypicking protocol](https://protocols.o This is an optional Part 2 protocol to its corresponding [Part 1: Normalization protocol using a multi-channel pipette](https://protocols.opentrons.com/protocol/6d901d) -**Note**: This protocol was updated for a change in our software stack and will require app 6.0 or greater. +**Note**: This protocol was updated for a change in our software stack and will require app 7.0 or greater. ![Cherrypicking Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/cherrypicking/cherrypicking_example.png) @@ -38,7 +38,7 @@ Explanation of complex parameters below: --- ### Labware -* Any verified labware found in our [Labware Library](https://labware.opentrons.com/?category=wellPlate) and some additional microplates (see plate options for source and destination plates parameters below, e.g. Greiner Bio-One plates) +* Any verified labware found in our [Labware Library](https://labware.opentrons.com/?category=wellPlate) and some additional microplates (see plate options for source and destination plates parameters below, e.g. Greiner Bio-One plates). ### Pipettes * [P20 Multi GEN2 Pipette](https://shop.opentrons.com/8-channel-electronic-pipette/) diff --git a/protocols/6d901d/6d901d.ot2.apiv2.py b/protocols/6d901d/6d901d.ot2.apiv2.py index 626f5c1ec..a2fc2507b 100644 --- a/protocols/6d901d/6d901d.ot2.apiv2.py +++ b/protocols/6d901d/6d901d.ot2.apiv2.py @@ -1,5 +1,5 @@ from opentrons import protocol_api -from opentrons import types +from opentrons.types import Mount metadata = { 'protocolName': 'Normalization with a multi-channel pipette \ @@ -22,7 +22,7 @@ def flatten_matrix(m): def well_csv_to_list(csv_string): """ - Takes a csv string and flattens it to a list, re-ordering to match + Takes a csv string and flattens to a list, re-ordering to match Opentrons well order convention (A1, B1, C1, ..., A2, B2, B2, ...) """ data = [ @@ -70,12 +70,19 @@ def run(ctx: protocol_api.ProtocolContext): m300 = ctx.load_instrument('p300_multi_gen2', p300_mount) m20 = ctx.load_instrument('p20_multi_gen2', p20_mount) - mounted_on = {"left": types.Mount.LEFT, "right": types.Mount.RIGHT} - - pick_up_current = 0.15 # 150 mA for single tip - ctx._hw_manager.hardware._attached_instruments[ - mounted_on[m20.mount]].update_config_item( - 'pick_up_current', pick_up_current) + if not ctx.is_simulating(): + pick_up_current = 0.1 # 100 mA for single tip + # Uncomment the next two lines if using Opentrons Robot Software version 7.1.x. # noqa:E501 + # Comment them if NOT using 7.1.x + for pipette in [m20, m300]: + ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pipette.mount)).update_config_item( # noqa:E501 + {'pick_up_current': {8: pick_up_current}}) + + # Uncomment the next two lines if using Opentrons Robot Software version 7.2.x # noqa:E501 + # Comment them if NOT using 7.2.x + # for pipette in [m20, m300]: + # ctx._hw_manager.hardware.get_pipette(Mount.string_to_mount(pipette.mount)).update_config_item( + # {'pick_up_current': pick_up_current}) tip300ctr = 95 tip20ctr = 95 diff --git a/protocols/6d901d/README.md b/protocols/6d901d/README.md index 431362028..0d885f99f 100644 --- a/protocols/6d901d/README.md +++ b/protocols/6d901d/README.md @@ -16,11 +16,11 @@ ## Description ![Normalization Example](https://opentrons-protocol-library-website.s3.amazonaws.com/custom-README-images/normalization/normalization_example.png) -Concentration 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](https://protocols.opentrons.com/protocol/normalization), that instead uses a multi-channel pipette as single channel pipette by picking up one tip at a time. +Concentration 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](https://protocols.opentrons.com/protocol/normalization), that instead uses a multi-channel pipette as single channel pipette by picking up one tip at a time. There is an optional [Part 2: Cherrypicking Protocol](https://protocols.opentrons.com/protocol/6d901d-2) to this protocol which performs cherrypicking using a multi-channel pipette in the same way. -**Note**: This protocol was updated for a change in our software stack and will require app 6.0 or greater. +**Note**: This protocol was updated for a change in our software stack and requires app 7.0 or greater. Using the customization fields below, set up your protocol. * `Volumes CSV`: Your input CSV specifying the normalization volumes. See the Setup section below for details. diff --git a/protocols/Opentrons_Logo/README.md b/protocols/Opentrons_Logo/README.md index f1c5c9971..737ed5980 100644 --- a/protocols/Opentrons_Logo/README.md +++ b/protocols/Opentrons_Logo/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/opentrons_logo). This page won’t be available after March 31st, 2024. ## Categories * Getting Started diff --git a/protocols/cherrypicking/README.md b/protocols/cherrypicking/README.md index 67d8f7fe6..3706a1531 100644 --- a/protocols/cherrypicking/README.md +++ b/protocols/cherrypicking/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/cherrypicking). This page won’t be available after March 31st, 2024. ## Categories * Featured diff --git a/protocols/customizable_serial_dilution_ot2/README.md b/protocols/customizable_serial_dilution_ot2/README.md index c6a2338da..d58d92c0d 100644 --- a/protocols/customizable_serial_dilution_ot2/README.md +++ b/protocols/customizable_serial_dilution_ot2/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/customizable_serial_dilution_ot2). This page won’t be available after March 31st, 2024. ## Categories * Featured diff --git a/protocols/dinosaur/README.md b/protocols/dinosaur/README.md index 7ba67e8a4..ea6cabaef 100644 --- a/protocols/dinosaur/README.md +++ b/protocols/dinosaur/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/dinosaur). This page won’t be available after March 31st, 2024. ## Categories * Getting Started diff --git a/protocols/illumina-nextera-XT-library-prep-part1/README.md b/protocols/illumina-nextera-XT-library-prep-part1/README.md index 2c70950ec..5fe84ed33 100644 --- a/protocols/illumina-nextera-XT-library-prep-part1/README.md +++ b/protocols/illumina-nextera-XT-library-prep-part1/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/illumina-nextera-xt-library-prep-part1). This page won’t be available after March 31st, 2024. ## Categories * Featured diff --git a/protocols/illumina-nextera-XT-library-prep-part2/README.md b/protocols/illumina-nextera-XT-library-prep-part2/README.md index e01b61987..8467c4b86 100644 --- a/protocols/illumina-nextera-XT-library-prep-part2/README.md +++ b/protocols/illumina-nextera-XT-library-prep-part2/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/illumina-nextera-xt-library-prep-part2). This page won’t be available after March 31st, 2024. ## Categories * Featured diff --git a/protocols/macherey-nagel-nucleomag-DNA-microbiome/README.md b/protocols/macherey-nagel-nucleomag-DNA-microbiome/README.md index 932640ec6..077a1fb50 100644 --- a/protocols/macherey-nagel-nucleomag-DNA-microbiome/README.md +++ b/protocols/macherey-nagel-nucleomag-DNA-microbiome/README.md @@ -3,7 +3,6 @@ ### Author [MACHEREY-NAGEL](https://www.mn-net.com/us) - ### Partner [Opentrons](https://opentrons.com/) diff --git a/protocols/macherey-nagel-nucleomag-clean-up/README.md b/protocols/macherey-nagel-nucleomag-clean-up/README.md index 8a43e76bd..729472ec1 100644 --- a/protocols/macherey-nagel-nucleomag-clean-up/README.md +++ b/protocols/macherey-nagel-nucleomag-clean-up/README.md @@ -3,7 +3,6 @@ ### Author [MACHEREY-NAGEL](https://www.mn-net.com/us) - ### Partner [Opentrons](https://opentrons.com/) diff --git a/protocols/macherey-nagel-nucleomag-dna-food/README.md b/protocols/macherey-nagel-nucleomag-dna-food/README.md index bbd09a4af..7d6f61e0f 100644 --- a/protocols/macherey-nagel-nucleomag-dna-food/README.md +++ b/protocols/macherey-nagel-nucleomag-dna-food/README.md @@ -3,7 +3,6 @@ ### Author [MACHEREY-NAGEL](https://www.mn-net.com/us) - ### Partner [Opentrons](https://opentrons.com/) diff --git a/protocols/macherey-nagel-nucleomag-tissue/README.md b/protocols/macherey-nagel-nucleomag-tissue/README.md index e06cee6ab..6a5593864 100644 --- a/protocols/macherey-nagel-nucleomag-tissue/README.md +++ b/protocols/macherey-nagel-nucleomag-tissue/README.md @@ -3,7 +3,6 @@ ### Author [MACHEREY-NAGEL](https://www.mn-net.com/us) - ### Partner [Opentrons](https://opentrons.com/) diff --git a/protocols/macherey-nagel-nucleomag-virus/README.md b/protocols/macherey-nagel-nucleomag-virus/README.md index 273ea7218..a9ed80132 100644 --- a/protocols/macherey-nagel-nucleomag-virus/README.md +++ b/protocols/macherey-nagel-nucleomag-virus/README.md @@ -3,7 +3,6 @@ ### Author [MACHEREY-NAGEL](https://www.mn-net.com/us) - ### Partner [Opentrons](https://opentrons.com/) diff --git a/protocols/normalization/README.md b/protocols/normalization/README.md index 5303742aa..a5d6e6bd4 100644 --- a/protocols/normalization/README.md +++ b/protocols/normalization/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/normalization). This page won’t be available after March 31st, 2024. ## Categories * Featured diff --git a/protocols/nucleic_acid_purification_with_magnetic_beads/README.md b/protocols/nucleic_acid_purification_with_magnetic_beads/README.md index 7fd492870..01c3b44c5 100644 --- a/protocols/nucleic_acid_purification_with_magnetic_beads/README.md +++ b/protocols/nucleic_acid_purification_with_magnetic_beads/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://https://library.opentrons.com/p/nucleic_acid_purification_with_magnetic_beads). This page won’t be available after March 31st, 2024. ## Categories * Featured diff --git a/protocols/omega_biotek_magbind_totalpure_NGS/README.md b/protocols/omega_biotek_magbind_totalpure_NGS/README.md index c44d4a310..1f0b257ca 100644 --- a/protocols/omega_biotek_magbind_totalpure_NGS/README.md +++ b/protocols/omega_biotek_magbind_totalpure_NGS/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -### Partner [Omega Bio-tek](http://omegabiotek.com/store/) # Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/omega_biotek_magbind_totalpure_ngs). This page won’t be available after March 31st, 2024. diff --git a/protocols/pcr_prep_part_1/README.md b/protocols/pcr_prep_part_1/README.md index 5c2b3b48e..74e0f2039 100644 --- a/protocols/pcr_prep_part_1/README.md +++ b/protocols/pcr_prep_part_1/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/pcr_prep_part_1). This page won’t be available after March 31st, 2024. ## Categories * PCR diff --git a/protocols/pcr_prep_part_2/README.md b/protocols/pcr_prep_part_2/README.md index 1e0a85aa5..2a8582338 100644 --- a/protocols/pcr_prep_part_2/README.md +++ b/protocols/pcr_prep_part_2/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/pcr_prep_part_2). This page won’t be available after March 31st, 2024. ## Categories * PCR diff --git a/protocols/sci-macherey-nagel-nucleomag/README.md b/protocols/sci-macherey-nagel-nucleomag/README.md index 916758218..0d6b402a7 100644 --- a/protocols/sci-macherey-nagel-nucleomag/README.md +++ b/protocols/sci-macherey-nagel-nucleomag/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-macherey-nagel-nucleomag). This page won’t be available after March 31st, 2024. ## Categories * Nucleic Acid Extraction & Purification diff --git a/protocols/sci-mag-bind-blood-tissue-kit/README.md b/protocols/sci-mag-bind-blood-tissue-kit/README.md index 477bd4403..9ca935574 100644 --- a/protocols/sci-mag-bind-blood-tissue-kit/README.md +++ b/protocols/sci-mag-bind-blood-tissue-kit/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-mag-bind-blood-tissue-kit). This page won’t be available after March 31st, 2024. ## Categories * Nucleic Acid Extraction & Purification diff --git a/protocols/sci-omegabiotek-extraction-fa/README.md b/protocols/sci-omegabiotek-extraction-fa/README.md index 44020f271..ee3f24e85 100644 --- a/protocols/sci-omegabiotek-extraction-fa/README.md +++ b/protocols/sci-omegabiotek-extraction-fa/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-omegabiotek-extraction-fa). This page won’t be available after March 31st, 2024. ## Categories * Nucleic Acid Extraction & Purification diff --git a/protocols/sci-omegabiotek-magbind-total-rna-96/README.md b/protocols/sci-omegabiotek-magbind-total-rna-96/README.md index 2ce5b9f0e..6eaa59b6a 100644 --- a/protocols/sci-omegabiotek-magbind-total-rna-96/README.md +++ b/protocols/sci-omegabiotek-magbind-total-rna-96/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-omegabiotek-magbind-total-rna-96). This page won’t be available after March 31st, 2024. ## Categories * Nucleic Acid Extraction & Purification diff --git a/protocols/sci-omegabiotek-magbind/README.md b/protocols/sci-omegabiotek-magbind/README.md index f97da1ccc..7feec76a1 100644 --- a/protocols/sci-omegabiotek-magbind/README.md +++ b/protocols/sci-omegabiotek-magbind/README.md @@ -3,7 +3,6 @@ [Opentrons (verified)](https://opentrons.com/) # Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-omegabiotek-magbind). This page won’t be available after March 31st, 2024. - ## Categories * Nucleic Acid Extraction & Purification * RNA Extraction diff --git a/protocols/sci-promega-magazorb-dna-mini-prep-kit/README.md b/protocols/sci-promega-magazorb-dna-mini-prep-kit/README.md index 86328c8b8..b3c44600e 100644 --- a/protocols/sci-promega-magazorb-dna-mini-prep-kit/README.md +++ b/protocols/sci-promega-magazorb-dna-mini-prep-kit/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-promega-magazorb-dna-mini-prep-kit). This page won’t be available after March 31st, 2024. ## Categories * Nucleic Acid Extraction & Purification diff --git a/protocols/sci-zymo-directzol-magbead/README.md b/protocols/sci-zymo-directzol-magbead/README.md index 4b8debe8f..6e5b53718 100644 --- a/protocols/sci-zymo-directzol-magbead/README.md +++ b/protocols/sci-zymo-directzol-magbead/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -# Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/sci-zymo-directzol-magbead). This page won’t be available after March 31st, 2024. ## Categories * Nucleic Acid Extraction & Purification diff --git a/protocols/swift-2s-turbo-pt1/README.md b/protocols/swift-2s-turbo-pt1/README.md index 263ece7df..ea950bb16 100644 --- a/protocols/swift-2s-turbo-pt1/README.md +++ b/protocols/swift-2s-turbo-pt1/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -### Partner [Swift Biosciences](https://swiftbiosci.com/) # Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/swift-2s-turbo-pt1). This page won’t be available after March 31st, 2024. diff --git a/protocols/swift-fully-automated/README.md b/protocols/swift-fully-automated/README.md index a5ad64ed0..6c370dac3 100644 --- a/protocols/swift-fully-automated/README.md +++ b/protocols/swift-fully-automated/README.md @@ -3,7 +3,6 @@ ### Author [Opentrons (verified)](https://opentrons.com/) -### Partner [Swift Biosciences](https://swiftbiosci.com/) # Opentrons has launched a new Protocol Library. You should use the [new page for this protocol](https://library.opentrons.com/p/swift-fully-automated). This page won’t be available after March 31st, 2024.