Does the DepMap team have metadata on the susceptibility of different cell lines to lentiviral infection? It would be very useful to know how easy it is to infect different DepMap cell lines with lentiviral libraries, as some cell lines are very resistant to infection whereas others are highly susceptible.
This might get at what you’re looking for:
CRISPRInferredModelEfficacy.csv
Post-Chronos The estimates for the efficacy of all models in the different libraries-screen types, computed from the Chronos runs. Columns: - ModelID - Achilles-Avana-2D - Achilles-Humagne-CD-2D - Achilles-Humagne-CD-3D - Project-Score-KY
My recollection is that Chronos has an estimate for susceptibility to lentiviral infection (might use different language) and similarly an efficacy score for each guide. But others can chime in / correct me.
That’s right, however the efficacy estimate is just based on the depletion of the most depleting guides in the library at the last available timepoint. It does not really correspond to infection success, because the population is selected. Unfortunately DepMap has no records of this. You could try reaching out directly to the Genomics Perturbation Platform at the Broad Institute.
Thanks, I got the info I needed from the GPP folks!
