OT2 Modular Cloning (MoClo) and Transformation in E. coli Workflow

Material for OT2 Modular Cloning and Transformation in E. coli Workflow

This workflow enables end-to-end molecular cloning using the OT2 liquid handling robot by OpenTrons. This includes:

• Performing modular cloning (Golden Gate) reactions.
• Transforming plasmids into E. coli using heat shock.
• Plating cell transformations onto rectangular agar plates.

All code for this project is freely distributed for academic and commercial uses under the MIT license.

General Installation

1. Confirm that you have Python 3 installed.

2. Download OT2 APP from Opentrons' website.

3. Clone the GitHub repository to a local computer.

Modular Cloning, Cell Transformation, and Cell Plating

Getting Started

Users looking to implement the OT2 Modular Cloning and Transformation in E. coli workflow are encouraged to consult the instructions. If you are looking to contribute to this project, please raise an issue or pull request. Otherwise, feel free to reach out to rychen58.

Initial setup

1. Prepare 1 CSV file (which can be produced in Excel) representing input DNA plate map. The input DNA plate maps may contain up to 96 DNA fragments and vectors, 8 rows by 12 columns, with each cell containing the name for DNA parts and empty wells left blank. The CSV file should represent 96-well microplate format plates of DNA parts at the desire concentration chossen by the users.

2. Prepare 1 CSV file representing the combination list for combinations of parts to assemble, with each row representing one assembly. Each row should have N columns with the names of the parts to assemble (which must match the names in the plate maps of step 1).

Generating protocol

3. Run the OT2-MoClo/moclo_transformation/moclo_transform_generator.py using Python (e.g. typing python3 moclo_transform_generator.py in the command line). Select the plate map, combinations list, and an output folder for the protocol when prompted.

4. A protocol named moclo_transform_protocol.py should be saved in the output folder.

Authors

• Rita R. Chen - rychen58
• Nick Emery - emernic