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mpi2 / impc-production-tracker

This repository will host the code for the new and improved IMPC effort production tracker. This is a successor to iMits, which started life as the ESCell production tracking database for the IMPC project.
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Add embryo production to a CrisprAttempt #923

Open rwilson-ebi opened 3 years ago

rwilson-ebi commented 3 years ago

The field should contain the following information

embryo production (mating, superovulation & mating, IVF)

Email from LN: March 3, 2021 at 2:05 PM

Hi All, I thought we had agreed to capture the variable information related to centre-specific protocols. To my mind, these variables are as follows. I include the ones that have proven useful for our analysis of the production data and therefore likely to be of use to have stored in the database rather than having to pull out from centre-specific protocols for global data analysis.

Protocol ID (of the centre-specific protocol used for production)

mode of delivery (pronuclear injection, cytoplasmic injection, electroporation)

embryo stage (zygote, 2-cell) embryo production (mating, superovulation & mating, IVF)

endonuclease type (expression plasmid, mRNA, protein, transgene) endonuclease concentration (currently in ng/µL, I would prefer to see µM)

gRNA concentration(s) (currently in ng/µL, I would prefer to see µM) gRNA sequence(s)

template sequence(s), if any template concentration(s) (currently in ng/µL, I would prefer to see µM) template format (ssoligo, long ssDNA, plasmid DNA, biotinylated or not, etc., unless we want to capture template format in different Centre-specific protocols)

Number of embryos treated Number of embryos transferred

Things like voltage, pulse length/width, interval, volumes of buffers and reagents, etc., should be fixed and available from the Centre-specific protocol. If it will be useful, I can put together what TCP would have as an example of a centre-specific protocol and we can discuss at a WG meeting what should be fixed (and when changed require a new protocol), and what could be variable (and therefore recorded in GenTaR).

We may also want to include some N1 QC options for Cas9 alleles which are different from ES cell alleles. Such as allele sequencing (which should be, in my view, a mandatory field for marking GLT) and then optional QC’s such as loss-of-allele assay (for deletion alleles), template copy number (when applicable), off-target analysis (target site and method), Cre-mediate recombination (for floxed alleles), mRNA analysis (e.g. tissue source, type of analysis (qrtPCR, dd-rtPCR, Northern, rtPCR, with ability to upload a file showing assay parameters like primers and probes used and the results?), protein analysis (e.g. by mass spec, Western blot, immunohistochemistry, others?). Any others?

The QC information could also enable us to add in feedback from the community, e.g. by summarizing the results to RNA or protein analysis and adding a PMID or file for the data.

albags commented 3 years ago

This ticket relates to protocol specifications.