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Delve Therapeutics Public Transcriptic Protocols

This is a set of transcriptic package protocols.

Protocol Overview

###Bacteria Freezing: Take bacteria from a well, amplify it, freeze (-80C) 10 tubes w/ 115ul each of it. Requires tubes to have a property "cell_line_name" with the name of the bacteria cell line. ###Bacteria Pelleting: Take bacteria from a well, amplify it, possibly induce to high copy number, and pellet ###DNA Resuspension: Add TE to a tube with DNA, mix, measure concentration, and optionally split the tube (-80C) into a 4C storage working stock ###Create Water Container: Handy test protocol to mimick reagent containers in test mode by making a container with every well filled to max volume with water ###Anneal Oligos and Ligate to Vector Anneal two oligos together and then ligate to a linearized vector. Vector must have 'Concentration (DNA)' property like '4.0:nanograms/microliter'. Includes the ability to optionally run a transform, spread, and pick afterwards (same protocol as the Transcriptic version). ###Miniprep More powerful miniprep than built in transcriptic version. Ability to set incubation time. Ability to 8x concentrate DNA (slow growht). Ability to induce high copy number in BAC. ###GelPurify Gel Purify a well with dna inside (e.g. after a PCR product). Includes concentration and purity measurement. Well must have a dna_length property (used for determining which band to extract). ###PCR Run PCR of a DNA template with two primers. Uses Q5 polymerase. Template well must have 'Concentration (DNA)' property like '4.0:nanograms/microliter'.

Use the NEB Tm calculator to determine the annealing temperature of your sequence - http://tmcalculator.neb.com/#!/

Running protocols from the command line (requires unix)

  1. update protocols/the_protocol/sample_input.json with the correct container id's you want to use
  2. update ~/.transcriptic to have your login credentials
{
 "api_root": "https://secure.transcriptic.com",
 "token": "your token",
 "email": "your email",
 "organization_id": "your org"
}
  1. Add the following to src/auth.json
{
 "X_User_Email":"your email",
 "X_User_Token":"your user token",
 "org_name": "your org name"
}
  1. Add the following to src/test_mode_auth.json (used for submitting test jobs)
{
 "X_User_Email":"your email",
 "X_User_Token":"your user test token",
 "org_name": "your org name"
}
  1. Run the protocol from the src dir
cd src
python protocols/bacteria_pelleting/protocol.py protocols/bacteria_pelleting/sample_input.json

Publishing packages (requires unix)

You can add the packages to your transcriptic UI (allowing users to use them through the web UI).

  1. Create a package by clicking "packages" and then "create new package" here https://secure.transcriptic.com/

  2. Run the following commands from the build dir

python set_test_mode_false.py
bash make_zip.sh
transcriptic upload-release release.zip "YourPackageName"