Using DepMap transcriptomic data to select a cell line where a gene is not expressed

Hi! I am working to select a cell line for a functional study, and am looking for a cell line that doesn’t express the target gene, so we can test the effect of mutant genes. Is there a common process that is used for this?

Right now, I am just sorting by expression, filtering for the tissue type we are interested in, CNS/Brain, and checking against the DepMap proteomic screen data for cell lines where it is available. Is this a common approach?


DepMap doesn’t have a specific built-in process on the portal, but that sounds like a reasonable approach!


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