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|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| { | ||
| "content": "import math\n\nmetadata = {\n 'protocolName': 'ELISA',\n 'author': 'Alise <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.13'\n}\n\n\ndef run(ctx):\n [number_of_standards, concentration_csv] = get_values( # noqa: F821\n 'number_of_standards', 'concentration_csv')\n\n # labware setup\n tuberack_4 = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4')\n deep_plates = [ctx.load_labware('nest_96_wellplate_2ml_deep', slot)\n for slot in ['5', '6']]\n trough = ctx.load_labware('nest_12_reservoir_15ml', '8')\n plate = ctx.load_labware(\n 'corning_96_wellplate_360ul_flat', '9')\n\n tipracks_300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['3', '10']]\n tiprack_m300 = ctx.load_labware('opentrons_96_tiprack_300ul', '7')\n\n # instrument setup\n m300 = ctx.load_instrument(\n 'p300_multi_gen2',\n mount='left',\n tip_racks=[tiprack_m300])\n p300 = ctx.load_instrument(\n 'p300_single',\n mount='right',\n tip_racks=tipracks_300)\n\n # reagent setup\n tubes = [well for row in tuberack_4.rows() for well in row]\n water = tubes[0]\n diluent = tubes[1]\n standards = tubes[2:2 + number_of_standards]\n samples = tubes[2 + number_of_standards:]\n antibody = trough.wells('A1')\n\n # define elution pool\n dil_dests = [row for deep_plate in deep_plates\n for row in deep_plate.rows()]\n conc_lists = [[int(cell) for cell in line.split(',') if cell]\n for line in concentration_csv.splitlines() if line]\n concs = [5, 10, 25, 50, 100, 500, 1000, 5000, 10000, 25000, 50000, 100000]\n\n samples = [\n row[concs.index(conc)]\n for concentrations, row in zip(conc_lists, dil_dests)\n for conc in concentrations\n ]\n\n dests = [\n [plate.columns()[index][num], plate.columns()[index+1][num]]\n for index in range(0, 12, 2) for num in range(8)\n ]\n\n \"\"\"\n Adding Enzyme Conjugate Reagent\n \"\"\"\n num_cols = math.ceil((2 + number_of_standards + len(samples)) / 8) * 2\n m300.distribute(100, antibody,\n plate.columns()[:num_cols], blow_out=antibody)\n\n \"\"\"\n Adding Water\n \"\"\"\n p300.distribute(50, water, dests[0])\n dests.pop(0)\n\n \"\"\"\n Adding Dilution Buffer\n \"\"\"\n p300.distribute(50, diluent, dests[0])\n dests.pop(0)\n\n \"\"\"\n Adding HCP Standards\n \"\"\"\n for standard in standards:\n p300.distribute(50, standard, dests[0])\n dests.pop(0)\n\n \"\"\"\n Adding Samples\n \"\"\"\n for sample in samples:\n p300.pick_up_tip()\n p300.aspirate(130, sample)\n for dest in dests[0]:\n p300.dispense(50, dest)\n p300.drop_tip()\n dests.pop(0)\n", | ||
| "content": "import math\n\nmetadata = {\n 'protocolName': 'Antibody Addition',\n 'author': 'Alise <[email protected]>',\n 'source': 'Custom Protocol Request',\n 'apiLevel': '2.14'\n}\n\n\ndef run(ctx):\n [number_of_standards, concentration_csv] = get_values( # noqa: F821\n 'number_of_standards', 'concentration_csv')\n\n # labware setup\n tuberack_4 = ctx.load_labware(\n 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4')\n deep_plates = [ctx.load_labware('nest_96_wellplate_2ml_deep', slot)\n for slot in ['5', '6']]\n trough = ctx.load_labware('nest_12_reservoir_15ml', '8')\n plate = ctx.load_labware(\n 'corning_96_wellplate_360ul_flat', '9')\n\n tipracks_300 = [ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n for slot in ['3', '10']]\n tiprack_m300 = ctx.load_labware('opentrons_96_tiprack_300ul', '7')\n\n # instrument setup\n m300 = ctx.load_instrument(\n 'p300_multi_gen2',\n mount='left',\n tip_racks=[tiprack_m300])\n p300 = ctx.load_instrument(\n 'p300_single',\n mount='right',\n tip_racks=tipracks_300)\n\n # reagent setup\n tubes = [well for row in tuberack_4.rows() for well in row]\n water = tubes[0]\n diluent = tubes[1]\n standards = tubes[2:2 + number_of_standards]\n samples = tubes[2 + number_of_standards:]\n antibody = trough.wells('A1')\n\n # define elution pool\n dil_dests = [row for deep_plate in deep_plates\n for row in deep_plate.rows()]\n conc_lists = [[int(cell) for cell in line.split(',') if cell]\n for line in concentration_csv.splitlines() if line]\n concs = [5, 10, 25, 50, 100, 500, 1000, 5000, 10000, 25000, 50000, 100000]\n\n samples = [\n row[concs.index(conc)]\n for concentrations, row in zip(conc_lists, dil_dests)\n for conc in concentrations\n ]\n\n dests = [\n [plate.columns()[index][num], plate.columns()[index+1][num]]\n for index in range(0, 12, 2) for num in range(8)\n ]\n\n \"\"\"\n Adding Enzyme Conjugate Reagent\n \"\"\"\n num_cols = math.ceil((2 + number_of_standards + len(samples)) / 8) * 2\n m300.distribute(100, antibody,\n plate.columns()[:num_cols], blow_out=antibody)\n\n \"\"\"\n Adding Water\n \"\"\"\n p300.distribute(50, water, dests[0])\n dests.pop(0)\n\n \"\"\"\n Adding Dilution Buffer\n \"\"\"\n p300.distribute(50, diluent, dests[0])\n dests.pop(0)\n\n \"\"\"\n Adding HCP Standards\n \"\"\"\n ctx.comment('hcp')\n for standard in standards:\n p300.distribute(50, standard, dests[0])\n dests.pop(0)\n\n \"\"\"\n Adding Samples\n \"\"\"\n for sample, chunk in zip(samples, dests):\n p300.pick_up_tip()\n p300.aspirate(130, sample)\n for well in chunk:\n p300.dispense(50, well)\n p300.drop_tip()\n # dests.pop(0)\n", | ||
| "custom_labware_defs": [], | ||
| "fields": [ | ||
| { | ||
|
|
@@ -82,9 +82,9 @@ | |
| } | ||
| ], | ||
| "metadata": { | ||
| "apiLevel": "2.13", | ||
| "apiLevel": "2.14", | ||
| "author": "Alise <[email protected]>", | ||
| "protocolName": "ELISA", | ||
| "protocolName": "Antibody Addition", | ||
| "source": "Custom Protocol Request" | ||
| }, | ||
| "modules": [] | ||
|
|
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@@ -5,12 +5,12 @@ | |
| "ELISA" | ||
| ] | ||
| }, | ||
| "description": "Links:\n Part 1: Dilution\n Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addition\nThis is the first part of a ELISA protocol: Dilution Procedure. The robot will perform serial dilutions samples located in the Opentrons 2 mL Eppendorf tube rack in the 1.2 mL tube plates. User will need to upload a CSV specifying the desired concentrations of each sample to be transferred to a separate 96-well plate in part 2 of the protocol. See more information on the CSV requirement in Additional Notes below.\nDownload full protocol details here.\n\nYou will need:\n P1000 Single-channel Pipette\n P300 Single-channel Pipette\n Opentrons Tube Racks (2 mL Eppendorf)\n Opentrons Tube Rack (15 + 50 mL)\n 2 mL 96-deep well Plate\n 96-well Plate\n 12-row Trough\n 1000 uL Tip Rack\n* 300 uL Tip Rack", | ||
| "description": "Links:\n Part 1: Dilution\n Part 2-1: Antibody Addition\n* Part 2-2: Substrate and Stop Solution Addition\nThis is the first part of a ELISA protocol: Dilution Procedure. The robot will perform serial dilutions samples located in the Opentrons 2 mL Eppendorf tube rack in the 1.2 mL tube plates. User will need to upload a CSV specifying the desired concentrations of each sample to be transferred to a separate 96-well plate in part 2 of the protocol. See more information on the CSV requirement in Additional Notes below.\nDownload full protocol details here.\n\nYou will need:\n P1000 Single-channel Pipette\n P300 Single-channel Pipette\n Opentrons Tube Racks (2 mL Eppendorf)\n Opentrons Tube Rack (15 + 50 mL)\n NEST 2 mL 96-deep well Plate\n 96-well Plate\n 12-row Trough\n 1000 uL Tip Rack\n* 300 uL Tip Rack", | ||
| "internal": "1464", | ||
| "markdown": { | ||
| "author": "[Opentrons](http://www.opentrons.com/)\n\n", | ||
| "categories": "* Proteins & Proteomics\n * ELISA\n\n", | ||
| "description": "Links:\n* [Part 1: Dilution](./1464)\n* [Part 2-1: Antibody Addition](./1464-2)\n* [Part 2-2: Substrate and Stop Solution Addition](1464-3)\n\nThis is the first part of a ELISA protocol: Dilution Procedure. The robot will perform serial dilutions samples located in the Opentrons 2 mL Eppendorf tube rack in the 1.2 mL tube plates. User will need to upload a CSV specifying the desired concentrations of each sample to be transferred to a separate 96-well plate in part 2 of the protocol. See more information on the CSV requirement in Additional Notes below.\n\n\nDownload full protocol details [here](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/1464-natrix-separations-inc-milliporesigma/NEW_ELISA_protocol.xlsx).\n\n---\n\nYou will need:\n* P1000 Single-channel Pipette\n* P300 Single-channel Pipette\n* [Opentrons Tube Racks (2 mL Eppendorf)](https://shop.opentrons.com/collections/opentrons-tips/products/tube-rack-set-1)\n* [Opentrons Tube Rack (15 + 50 mL)](https://shop.opentrons.com/collections/opentrons-tips/products/tube-rack-set-1)\n* [2 mL 96-deep well Plate](https://www.usascientific.com/2ml-deep96-well-plateone-bulk.aspx)\n* 96-well Plate\n* 12-row Trough\n* 1000 uL Tip Rack\n* 300 uL Tip Rack\n\n", | ||
| "description": "Links:\n* [Part 1: Dilution](./1464)\n* [Part 2-1: Antibody Addition](./1464-2)\n* [Part 2-2: Substrate and Stop Solution Addition](1464-3)\n\nThis is the first part of a ELISA protocol: Dilution Procedure. The robot will perform serial dilutions samples located in the Opentrons 2 mL Eppendorf tube rack in the 1.2 mL tube plates. User will need to upload a CSV specifying the desired concentrations of each sample to be transferred to a separate 96-well plate in part 2 of the protocol. See more information on the CSV requirement in Additional Notes below.\n\n\nDownload full protocol details [here](https://s3.amazonaws.com/opentrons-protocol-library-website/custom-README-images/1464-natrix-separations-inc-milliporesigma/NEW_ELISA_protocol.xlsx).\n\n---\n\nYou will need:\n* P1000 Single-channel Pipette\n* P300 Single-channel Pipette\n* [Opentrons Tube Racks (2 mL Eppendorf)](https://shop.opentrons.com/collections/opentrons-tips/products/tube-rack-set-1)\n* [Opentrons Tube Rack (15 + 50 mL)](https://shop.opentrons.com/collections/opentrons-tips/products/tube-rack-set-1)\n* NEST 2 mL 96-deep well Plate\n* 96-well Plate\n* 12-row Trough\n* 1000 uL Tip Rack\n* 300 uL Tip Rack\n\n", | ||
| "internal": "1464\n", | ||
| "notes": "Tube Rack setup: (slot 4)\n* DI Water: A1\n* Diluent: A2\n* HCP Standards: A3-B2 if number of standards is 6, A3-B4 if 8\n* Samples: B3-(D6) if number of standards is 6, B5-(D6) if 8\nYou will need to shift the locations of the samples based on the number of standards you have each run. This configuration must be consistent of that of part 2.\n\n---\n\nCSV Layout:\n\n\n\n* No headers\n* Each row represents each sample\n* Each column represents the dilution factor of that sample to be transferred to the output plate in part 2 of the protocol\n* Robot will determine the dilution scheme of each sample based on the concentrations in the CSV\n\n---\n\nIf you have any questions about this protocol, please contact [email protected].\n\n", | ||
| "process": "1. Download your protocol.\n2. Upload your protocol into the [OT App](https://opentrons.com/ot-app).\n3. Set up your deck according to the deck map.\n4. Calibrate your labware, tiprack and pipette using the OT App. For calibration tips, check out our [support article](https://support.opentrons.com/ot-2/getting-started-software-setup/deck-calibration).\n5. Hit \"Run\".\n\n\n", | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,10 @@ | ||
| import math | ||
|
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| metadata = { | ||
| 'protocolName': 'ELISA', | ||
| 'protocolName': 'Antibody Addition', | ||
| 'author': 'Alise <[email protected]>', | ||
| 'source': 'Custom Protocol Request', | ||
| 'apiLevel': '2.13' | ||
| 'apiLevel': '2.14' | ||
| } | ||
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@@ -83,17 +83,18 @@ def run(ctx): | |
| """ | ||
| Adding HCP Standards | ||
| """ | ||
| ctx.comment('hcp') | ||
| for standard in standards: | ||
| p300.distribute(50, standard, dests[0]) | ||
| dests.pop(0) | ||
|
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||
| """ | ||
| Adding Samples | ||
| """ | ||
| for sample in samples: | ||
| for sample, chunk in zip(samples, dests): | ||
| p300.pick_up_tip() | ||
| p300.aspirate(130, sample) | ||
| for dest in dests[0]: | ||
| p300.dispense(50, dest) | ||
| for well in chunk: | ||
| p300.dispense(50, well) | ||
| p300.drop_tip() | ||
| dests.pop(0) | ||
| # dests.pop(0) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,8 @@ | ||
| metadata = { | ||
| 'protocolName': 'ELISA', | ||
| 'protocolName': 'Substrate and Stop Solution Addition', | ||
| 'author': 'Alise <[email protected]>', | ||
| 'source': 'Custom Protocol Request', | ||
| 'apiLevel': '2.13' | ||
| 'apiLevel': '2.14' | ||
| } | ||
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@@ -29,18 +29,20 @@ def run(ctx): | |
| tip_racks=tiprack_m300) | ||
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| # reagent setup | ||
| TMB_substrate = trough.wells_by_name()['A6'] | ||
| stop_solution = trough.wells_by_name()['A12'] | ||
| TMB_substrate = trough.wells_by_name()['A6'].bottom(z=0) | ||
| stop_solution = trough.wells_by_name()['A12'].bottom(z=0) | ||
|
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| """ | ||
| Adding TMB substrate | ||
| """ | ||
| m300.pick_up_tip() | ||
| m300.distribute( | ||
| 100, | ||
| TMB_substrate.bottom(), | ||
| TMB_substrate, | ||
| [col[0].top() for col in plate.columns()[:number_of_columns]], | ||
| blow_out=TMB_substrate, | ||
| blow_out=False, | ||
| disposal_volume=0.05, | ||
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| new_tip='never') | ||
| m300.aspirate(20, plate.columns()[number_of_columns-1][0].top()) | ||
| m300.drop_tip() | ||
|
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@@ -52,5 +54,5 @@ def run(ctx): | |
| """ | ||
| for col in plate.columns()[:number_of_columns]: | ||
| m300.pick_up_tip() | ||
| m300.transfer(100, stop_solution.bottom(), col, new_tip='never') | ||
| m300.transfer(100, stop_solution, col, new_tip='never') | ||
| m300.drop_tip() | ||
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|---|---|---|
| @@ -1,10 +1,16 @@ | ||
| cimport math | ||
| def get_values(*names): | ||
| import json | ||
| _all_values = json.loads("""{"starting_buffer_volume":50,"number_of_standards":6,"concentration_csv":"50,500,5000\\n10,10000,100000\\n100,,\\n5,,"}""") | ||
| return [_all_values[n] for n in names] | ||
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| import math | ||
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| metadata = { | ||
| 'protocolName': 'ELISA: Dilution', | ||
| 'author': 'Alise <[email protected]>', | ||
| 'source': 'Custom Protocol Request', | ||
| 'apiLevel': '2.13' | ||
| 'apiLevel': '2.14' | ||
| } | ||
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@@ -19,7 +25,7 @@ def run(ctx): | |
| 'opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical', '1') | ||
| tuberack_4 = ctx.load_labware( | ||
| 'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap', '4') | ||
| deep_plates = [ctx.load_labware('plateone_96_wellplate_2000ul', slot) | ||
| deep_plates = [ctx.load_labware('nest_96_wellplate_2ml_deep', slot) | ||
| for slot in ['5', '6']] | ||
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| tiprack_1000 = ctx.load_labware('opentrons_96_tiprack_1000ul', '2') | ||
|
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@@ -47,9 +53,12 @@ def run(ctx): | |
| conc_lists = [[int(cell) for cell in line.split(',') if cell] | ||
| for line in concentration_csv.splitlines() if line] | ||
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| concs = [5, 10, 25, 50, 100, 500, 1000, 2500, 5000, 10000, 50000, 100000] | ||
| diluent_vols = [320, 450, 180, 320, 450, 320, 450, 180, 320, 450, 180, 450] | ||
| sample_vols = [80, 50, 120, 80, 50, 80, 50, 120, 80, 50, 80, 50] | ||
| concs = [5, 10, 25, 50, 100, 500, 1000, 5000, 10000, 25000, 50000, 100000] | ||
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| diluent_vols = [320, 450, 180, 320, 450, 320, 450, 320, 450, 180, 320, 450] | ||
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| sample_vols = [80, 50, 120, 80, 50, 80, 50, 80, 50, 120, 80, 50] | ||
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| concs_init = [1, 1, 10, 10, 10, 100, 100, 1000, 1000, 1000, 10000, 10000] | ||
| dil_formulae = { | ||
| conc: {'diluent_vol': diluent_vol, | ||
|
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@@ -82,14 +91,15 @@ def run(ctx): | |
| dilution_concs.append(new_concs) | ||
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| # transfer dilution buffer | ||
| p1000.pick_up_tip() | ||
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| for sample_index, (row, concs) in enumerate( | ||
| zip(dil_dests, dilution_concs)): | ||
| volumes = [dil_formulae[conc]['diluent_vol'] | ||
| for c_list in concs for conc in c_list] | ||
| dests = [row[dil_formulae[conc]['col_index']] | ||
| for c_list in concs for conc in c_list] | ||
| for volume, dest in zip(volumes, dests): | ||
| p1000.pick_up_tip() | ||
| buffer_height += volume / (math.pi * (13.5 ** 2)) | ||
| if buffer_height > 75: | ||
| source = dilution_buffer.bottom(3) | ||
|
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@@ -101,7 +111,7 @@ def run(ctx): | |
| dest.top(-20), | ||
| new_tip='never') | ||
| p1000.blow_out(dest.top()) | ||
| p1000.drop_tip() | ||
| p1000.drop_tip() | ||
|
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| # transfer samples | ||
| for sample_index, (row, concs) in enumerate( | ||
|
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