Categorization of Cell Lines by DepMap Release Date

Q&A
1

Hi all,
I’m trying to track the order of the addition of new cell lines to DepMap. I’d like to know what was the first release that included CRISPR screen data for a particular cell line, for the entire dataset. I do not see such a field in sample_info; is this data in metadata somewhere?

Cheers,
ben

2

No, we don’t report information about when a line was first added to the different datasets. Depending on what you are looking for, I can imagine this question might mean a few things. (For example, we have a CRISPR dataset which is harmonized data from both Broad and Sanger. Are you looking for the date it was screened by Broad or inclusion in any dataset?)

Regardless, the likely only way to get that information is to download the various CRISPR datasets from past release and compute the difference between each datasets and it’s prior release to see which lines were introduced new in that release. All past releases are downloadable from the portal, so it should be possible to reconstruct the history with those files if needed.

Thanks,
Phil

3

Thanks, I have started doing this manually as you suggested. Date/release # when a cell line was CRISPR-screened only by Broad would be very helpful if you happen to have this internally, but I’d take date included for the first time in any CRISPR dataset also.
Cheers,
Ben

p.s. The new Tools are really nice!