I want to utilize cell viability data after CRISPR treatment.
I guess ‘KYLogfoldChange’, ‘HumagneLogfoldChange’, ‘HumagneLogfoldChange’ data in 23Q4 are cell viability data.
But, ‘README’ says “Log2-fold-change from pDNA counts for each sequence screened with the Sanger’s KY Cas9 Library.” , so I’m confused .It is confusing whether it is data on the amount of change in a specific gene, not a cell.
please help me !
Perhaps the best place to start is reading this paper which largely describes how this data was generated Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines | bioRxiv
The short version is that file contains log fold change in abundances of guides. Those guides that are depleted are thought to have induced lethal knockouts, and thus, suggest the gene is essential in that specific cell line.
However, that is the raw data from the experiment and there are multiple known confounders that should be taken into account before trying to interpret those scores. If you’re interested in which genes are essential in which lines, you probably want to look at the files whose units are “Gene Effect” or “Probability of Dependency” instead. (See the paper liked above for details)
Thanks,
Phil
