Sep 25, 2023
Opentrons Pipeline: PCR Preparation
- Jhakelin Reyes Vasquez1,2,
- P. Sánchez-Vendizú3,4,2,
- Gideon Erkenswick5,
- Alexandra Sacco6,5,
- Mrinalini Watsa7,
- Thalía Silvestre8
- 1Imperial College London;
- 2Conservación Amazónica-ACCA;
- 3Universidad Austral de Chile;
- 4Universidad Nacional Mayor de San Marcos;
- 5Field Projects International;
- 6Washington University in Saint Louis;
- 7San Diego Wildlife Alliance;
- 8UNMSM
- In Situ LaboratoriesTech. support email: [email protected]
Protocol Citation: Jhakelin Reyes Vasquez, P. Sánchez-Vendizú, Gideon Erkenswick, Alexandra Sacco, Mrinalini Watsa, Thalía Silvestre 2023. Opentrons Pipeline: PCR Preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.rm7vzx6y8gx1/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
Created: September 22, 2023
Last Modified: September 25, 2023
Protocol Integer ID: 88226
Keywords: Opentrons, PCR, Mastermix, automated, insitulabs, OT2, opentrons pipeline, pcr preparation this protocol, pcr preparation, opentrons tips number of sample, sterile reagent, automated pipeline, opentron, filtered opentrons tips number, automated pipetting robot, pipeline, pipetting robot, mastermix at the plate level, pcr, ingredients open on the deck, open inside the ot2 hood, sterile way, process, robot, preparation, point pcr
Funders Acknowledgements:
Gordon and Betty Moore Foundation
Grant ID: 9772
Gordon and Betty Moore Foundation
Grant ID: 9776
Abstract
This protocol is a general automated pipeline to prepare mastermix at the plate level in a sterile way. The protocol volumes can be edited, as can sample numbers, to change the scale of the operation and optimise it to fit any end-point PCR.
This protocol was developed and optimised for the following:
- Platform: Opentrons OT-2 automated pipetting robot
- Tested with software version 6.3.1
- GoTaq G2 Hot Start Green Master MixPromegaCatalog #M742B
- Tips Used: 1 box and 1 column of 20uL filtered Opentrons Tips
- Number of samples: 91 samples and 5 controls in a 96 well plate
Important: In an ideal situation, there would be two OT-2 robots involved in this process: the first to prepare sterile reagents and make and aliquot the mastermix, and the second to add the template. In the absence of this facility, we have developed a means of keeping each ingredient on the deck singly, rather than having all ingredients open on the deck at once. So please take note of the protocol pauses in built to replace each ingredient with the next. In this way, no two ingredients are open inside the OT2 hood at the same time.
Python File Version 2.2.
Guidelines
Step 1: Please note we use a particular Taq but you can alter this to suit your needs. You can also edit your PCR mix recipe by following the template in this protocol.
Step 5: Import the labware file BEFORE you import your protocol or it will give an error. This protocol has been validated against Opentrons software app version 6.3.1
Step 10: Take note of the two possible ways of loading gDNA. A skirted plate will clip into the deck, and a non-skirted plate or strip tubes will need support (and the labware definition file attached to this protocol).
Step 12: Note that we have specific wells in which we load controls, and for this you will need to remove the tips from the box so no template is added accidentally. We then load our controls later in a PCR hood.
Materials
Protocol materials
Nuclease-Free Water-25mLPromegaCatalog #MC1191
GoTaq G2 Hot Start Green Master MixPromegaCatalog #M742B
10% Bleach
Distilled Water
70% Alcohol
Troubleshooting
Safety warnings
Use PPE to handle all samples and liquids. Make sure to open ALL ingredients outside the OT2 deck, and place the plates in the deck only after any aerosols have dispersed.
Before start
Clean the OT2 deck and walls with:
10% Bleach 1 rinse
Distilled Water 1 rinse
70% Alcohol 2 rinses
Note
Avoid wetting electronic parts.
Materials and reagents
Reagents List
GoTaq G2 Hot Start Green Master MixPromegaCatalog #M742B
Primers Forward and Reverse 10 micromolar (µM) or specific for each primer.
Nuclease-Free Water-25mLPromegaCatalog #MC1191
Materials List
2 X plate seals
1 x 1.5 mL microcentrifuge tube
Note
The thermocycler module is not a critical component of this protocol, but removing it would require the user to make some small modifications to the protocol and labware definitions indicating the location of the destination plate, and the plate type. You can prepare the plate and remove it and run it on any protocol.
Items to prepare in advance
Prepare your Master Mix following your specific protocol.
| A | B | C | D | E | |
| start [ ] | desired [ ] | Volume (uL) per reaction | Per 96 reactions | ||
| GoTaq G2 Hot Start Green Master Mix | 2X | 1X | 6.25 | 600 | |
| Forward Primer | Specific for each primer | Specific for each primer | Specific for each primer | ||
| Reverse Primer | Specific for each primer | Specific for each primer | Specific for each primer | ||
| Nuclease-Free Water | to reach 10.5 | ||||
| Mastermix volume per reaction | 10.5 | ||||
| Template | 2 | ||||
| Final volume | 12.5 | ||||
An example of a mastermix recipe.
Dispense Master Mix in all 8 wells of a 0.2mL PCR strip tube equally.
Total volume per strip tube well = MasterMix total volume divided by 8
Import the lab ware file to your Opentrons app: 
denville_96_aluminumblock_200ul.json25KB
denville_96_aluminumblock_200ul.json25KB Load python file to Opentrons app: Automated Opentrons Pipeline for PCR Preparation V2.2 ISL.py3KB
Automated Opentrons Pipeline for PCR Preparation V2.2 ISL.py3KB (Optional) Attach a P20 Gen 2 Single Pipette to the left pipette mount. Note this is not used in this protocol, but should you want to do less than a multiple of 8, you could edit the script to use this pipette to load those samples, potentially.
Arrange the OT-2 deck as follows for 96 samples in a plate:
Note
Keep the Aluminum Block cold until the protocol starts.
This slot is used for placing the master mix, and then later the genomic DNA template in a Nest skirted PCR Plate
Placement of Labware and Tips in the OT2 Deck for transferring samples and Master Mix.
Calibrate the deck in the Opentrons app and follow instructions on the app.
OT2 PCR script definitions
Master Mix
PCR Master Mix
Name in the Deck: MM
Labware name in the script protocol: MM_and_samples_plate
Variable name in the script: MMix
gDNA samples
Template DNA
Name in the Deck: gDNA cleaned samples
Labware name in the protocol: MM_and_samples_plate
Variable name in the script: template
PCR samples
Destination for template + Master Mix
Name in the Deck: PCR plate
Labware name in the script protocol: final_PCR_plate
Variable name in the script: pcr_samples
Protocol variables definition
The following variables can be edited within the python script in a text editor program to fit your specific PCR setup needs, by changing the "MM_vol" and "template_vol" definitions in the third line of the script.
The default protocol is written to use 2 µL of Template + 10.5 µL of Master Mix to reach 12.5 µL as final volume.
Standard protocol variable definitions:
"sample_number" indicates the number of samples that you will process: 96
"MM_vol" indicates the volume of Master Mix per well: 10.5
"template_vol" indicates the template volume added to each well: 2
Note
It is better if sample_number is a multiple of 8 given that the OT-2 uses a multichannel pipettes for transferring samples
OT2 Protocol: Transferring mastermix and samples
Transferring Master Mix to final_PCR_plate
- Place the PCR strip tube (already containing the MasterMix) in the first column of the 96-well Aluminum Block
10.5 µL of Master Mix is transferred from the PCR strip tube in the aluminum block in Slot 1 to the PCR plate in the Opentrons Thermocycler Module - GEN2 in Slot 7
Note: Only the first column of tips in the Slot 6 rack is used for dispensing Master Mix to all columns of PCR plate.
- Once this step is finished the robot will PAUSE. During this PROTOCOL PAUSE, carefully remove the PCR strip tube of MasterMix and now replace it with the plate of gDNA.
Note
You have two options here:
1. Either load your gDNA in a skirted NEST 100uL plate, which will clip into Slot 1, after you remove the aluminum block. If you do, you don't need the additional labware definition we have provided, and can simply edit the script to give the definition of the NEST plate (available on the
OR
2. Leave the aluminum block in, and add
Both products linked above will fit the labware definition provided in this protocol.
Then, resume the run to continue with Step 11.
Transferring gDNA samples to final_PCR_plate
2 µL of template are transferred from MM_and_samples_plate in Slot 1 to final_PCR_plate in Opentrons Thermocycler Module - GEN2
Tips in Slot 3 are used for this step
Note
IMPORTANT NOTE: Take out tips in Slot 3 for established positions for controls:
Negative controls: Positions G3, B10
Positive controls: Positions B3, G10
Sample control: D6
Note
Samples are mixed in this step before and after transferring.
Note: Once finished, cover the plate with a seal to move it into the PCR cabinet to add the controls.
Manually adding controls
Adding controls
Add the controls in a sterile PCR cabinet, in the following pre-determined spaces.
| 1 | 2 | 3 | 4 | 5 | |
| A | |||||
| B | Positive control | ||||
| C | |||||
| D | |||||
| E | |||||
| F | |||||
| G | Negative control | ||||
| H |
| 1 | 2 | 3 | 4 | 5 | |
| A | |||||
| B | Positive control | ||||
| C | |||||
| D | Sample control | ||||
| E | |||||
| F | |||||
| G | Negative control | ||||
| H |
| 1 | 2 | |
| A | ||
| B | ||
| C | ||
| D | ||
| E | ||
| F | ||
| G | ||
| H |
The PCR plate is now ready to be loaded into a thermal cycler.
CLEANUP
Clean the OT2 deck and walls with:
10% Bleach 1 rinse
Distilled Water 1 rinse
70% Alcohol 2 rinses
Note
Avoid wetting any electronic parts.
Clean OT2 module with:
70% Alcohol 2 rinses
Note
Avoid wetting electronic parts.
Air dry OT2 robot and modules.