Merge pull request #4820 from Opentrons/develop

chore(Release): 2023-08-03

Author: ncdiehl11

data/data/fields.csv

@@ -152,7 +152,7 @@ cd8_dil,1
 cdna_col_num1,1
 cdna_col_num2,1
 cdna_down_column,1
-cdna_vol,1
+cdna_vol,2
 cellht,1
 cellsmedia,1
 change_standard_tip,1
@@ -569,7 +569,7 @@ init_vol_sds,2
 init_vols_csv,1
 initial_denaturation_cycles,1
 initial_vol,1
-input_csv,22
+input_csv,23
 input_file,10
 input_file2,6
 input_labware,1
@@ -874,10 +874,10 @@ num_curves,1
 num_daughter_plates,1
 num_drug_plates,1
 num_extracts,1
-num_gene,1
+num_gene,2
 num_lw,1
 num_mag_beads_tubes,1
-num_mastermix,3
+num_mastermix,4
 num_mixes,1
 num_mm,2
 num_of_dilutions,2
@@ -893,7 +893,6 @@ num_rounds,1
 num_row,1
 num_rows_a,1
 num_rows_b,1
-num_rxns,1
 num_samp,69
 num_samp_p1,1
 num_samp_p2,1
@@ -964,7 +963,7 @@ p1kmnt,1
 p1n,1
 p1num,1
 p20_blowout_height,1
-p20_mount,131
+p20_mount,133
 p20_multi_mount,3
 p20_rate,2
 p20_reservoir_height,1
@@ -1181,7 +1180,7 @@ reservoir_loc,1
 reservoir_slot,1
 reservoir_type,5
 reset_counter,1
-reset_tipracks,6
+reset_tipracks,7
 resettips,1
 resv_well_edge_offset,1
 return_tips,1
@@ -1281,6 +1280,7 @@ serial_dil_facta,1
 serial_dil_factb,1
 serial_dil_factc,1
 serial_dil_factd,1
+serum_vol,1
 set_tip_max,2
 settling_1,1
 settling_2,1

protoBuilds/0045f1/README.json

@@ -6,7 +6,7 @@
         ]
     },
     "deck-setup": "\n",
-    "description": "This protocol spots up to 6 slides with antibody. Each slide has 8 wells, to which the protocol will spot with 8 dots for wells 2-7. The user has the ability to manipulate the spacing between the dots, as well as the volume of the dispenses. The user can also specify the number of slides spotted. Please see below for the order in which slides are spotted.\nExplanation of complex parameters below:\n Number of tubes: Specify the number of tubes this protocol will run.\n Number of Slides: Specify the number of slides for this run (1-6).\n Spot Spacing: Specify the spacing between dots on the slide wells.\n Spot Volume: Specify the volume of each dot.\n Aspiration Flow Rate: Specify the aspiration rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n Dispense Flow Rate: Specify the dispense rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* P20 Single-Channel Mount: Specify which mount (left or right) to host the P20 single-channel pipette.\n",
+    "description": "This protocol spots up to 6 slides with antibody. Each slide has 8 wells, to which the protocol will spot with 8 dots for wells 2-7. The user has the ability to manipulate the spacing between the dots, as well as the volume of the dispenses. The user can also specify the number of slides spotted. Please see below for the order in which slides are spotted.\nExplanation of complex parameters below:\n* Number of tubes: Specify the number of tubes this protocol will run.\n* Number of Slides: Specify the number of slides for this run (1-6).\n* Spot Spacing: Specify the spacing between dots on the slide wells.\n* Spot Volume: Specify the volume of each dot.\n* Aspiration Flow Rate: Specify the aspiration rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* Dispense Flow Rate: Specify the dispense rate. A value of 1 is the default rate, a value of 1.2 is a 20% increase of the default rate, a value of 0.5 is half of the default rate.\n* P20 Single-Channel Mount: Specify which mount (left or right) to host the P20 single-channel pipette.\n",
     "internal": "0045f1",
     "labware": "\nOpentrons 10ul filter tips\nOpentrons 4-in-1 tube rack with Eppendorf 1.5mL safelock snapcap\nCustom slide plate\n",
     "markdown": {

protoBuilds/00a214-protocol-1/README.json

@@ -5,7 +5,7 @@
             "Seeding Plate"
         ]
     },
-    "description": "This protocol automates seeding plates with mammalian cells and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 8 plates, the protocol will iterate through each plate and remove 50\u00b5L before adding 140\u00b5L from the reservoir. Each plate should have a designated well in the 12-well trough (i.e., slot 1 --> plate 1, slot 2 --> plate 2, etc.)\n\nIf you have any questions about this protocol, please email our Applications Engineering team at [email protected].\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at [email protected]\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Eppendorf Plate (Plate 3)\n\nSlot 5: Eppendorf Plate (Plate 4)\n\nSlot 6: Eppendorf Plate (Plate 5)\n\nSlot 7: Eppendorf Plate (Plate 6)\n\nSlot 8: Eppendorf Plate (Plate 7)\n\nSlot 9: Eppendorf Plate (Plate 8)\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-8) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n",
+    "description": "This protocol automates seeding plates with mammalian cells and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 8 plates, the protocol will iterate through each plate and remove 50\u00b5L before adding 140\u00b5L from the reservoir. Each plate should have a designated well in the 12-well trough (i.e., slot 1 --> plate 1, slot 2 --> plate 2, etc.)\n\nIf you have any questions about this protocol, please email our Applications Engineering team at [email protected].\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at [email protected]\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 4: Eppendorf Plate (Plate 3)\n\nSlot 5: Eppendorf Plate (Plate 4)\n\nSlot 6: Eppendorf Plate (Plate 5)\n\nSlot 7: Eppendorf Plate (Plate 6)\n\nSlot 8: Eppendorf Plate (Plate 7)\n\nSlot 9: Eppendorf Plate (Plate 8)\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-8) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n",
     "internal": "00a214-protocol-1",
     "markdown": {
         "author": "[Opentrons](https://opentrons.com/)\n\n",

protoBuilds/00a214-protocol-2/README.json

@@ -5,7 +5,7 @@
             "Staining"
         ]
     },
-    "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at [email protected].\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at [email protected]\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-4) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n",
+    "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at [email protected].\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at [email protected]\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-4) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n",
     "internal": "00a214-protocol-2",
     "markdown": {
         "author": "[Opentrons](https://opentrons.com/)\n\n",

protoBuilds/00a214-protocol-3/README.json

@@ -5,7 +5,7 @@
             "Staining"
         ]
     },
-    "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at [email protected].\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at [email protected]\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n Number of Plates: Specify the number of plates (1-4) to use.\n Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n",
+    "description": "This protocol automates DAPI staining and is part of a five protocol suite. The five protocols are:\n\nProtocol 1: Seeding Plates with Mammalian Cells\nProtocol 2: DAPI Staining\nProtocol 3: Fix and DAPI Stain\nProtocol 4: Media Exchange\nProtocol 5: Primary Staining\n\nThe protocol begins with an empty reservoir for liquid waste, a 12-channel reservoir that contains what will be added to the plates, tips, eppendorf plate(s), and the P300-Multi attached to the left mount. Using up to 4 plates, the protocol will iterate through each plate, adding reagents to the plate and removing liquid.\n\nThe following steps are performed to each plate:\nRemove 120\u00b5L of media\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 100\u00b5L of 2% PFA\nPause\nRemove 100\u00b5L of 2% PFA\nAdd 140\u00b5L of PBS+DAPI\nRemove 140\u00b5L of PBS+DAPI\nAdd 140\u00b5L of PBS\nRemove 140\u00b5L of PBS\nAdd 140\u00b5L of PBS\n\nIf you have any questions about this protocol, please email our Applications Engineering team at [email protected].\n\n\nTo purchase tips, reagents, or pipettes, please visit our online store or contact our sales team at [email protected]\n\nOpentrons OT-2\nOpentrons OT-2 Run App (Version 3.19.0 or later)\nOpentrons p300 Multi-Channel Pipette, GEN2\nOpentrons Tips\nNEST 12-Well Reservoir, 15mL\nNEST 1-Well Reservoir, 195mL\nEppendorf Plate\nReagents\n\n\n\nSlot 1: Opentrons Tips, note: protocol saves tip state and will prompt user to replace tips when new tips are needed.\n\nSlot 2: Eppendorf Plate (Plate 1)\n\nSlot 3: Eppendorf Plate (Plate 2)\n\nSlot 5: Eppendorf Plate (Plate 3)\n\nSlot 6: Eppendorf Plate (Plate 4)\n\nSlot 7: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS\nColumns 5-8: PBS\nColumns 9-12: 2% PFA\n\nSlot 10: NEST 12-Well Reservoir, 15mL\n\nColumns 1-4: PBS+DAPI\nColumns 5-8: PBS\nColumns 9-12: PBS\n\nSlot 11: NEST 1-Well Reservoir, 195mL, for liquid waste\n\nNote: When filling the 12-well reservoirs with reagents, each column corresponds to a plate (there are 4 columns allocated per reagent). For example, if running this protocol with two (2) plates, columns 1, 2, 5, and 6 would be filled with PBS in slot 7; columns 9 and 10 would be filled with 2% PFA; etc.\n\nUsing the customizations field (below), set up your protocol.\n* Number of Plates: Specify the number of plates (1-4) to use.\n* Aspiration/Dispense Speed: Specify the aspiration/dispense speed of the pipette (in \u00b5L/sec). Note: default rate is 43.46\u00b5L/sec.\n* Aspiration Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when aspirating.\n* Dispense Height: Specify how high (in mm) from the bottom of the well the pipette should be in the plate when dispensing.\n\n",
     "internal": "00a214-protocol-3",
     "markdown": {
         "author": "[Opentrons](https://opentrons.com/)\n\n",