Add ability to store a protocol to GenTaR

[rwilson-ebi]

Add the means to associate a protocol with a production attempt

[] Upload a protocol
[] Display protocols relevant to the centre when creating a new production plan
[] Have the ability to manage different versions of a protocol
[] Require an example of a protocol (TCP will provide this)

Email from user: 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.