I was wondering if it is possible to download/extract the complete expression profile of a specific gene knock-down experiment for all available/processed cell-lines. So fare I was only able to find genearl expression profiles for cell-lines within the download section.
Thx a lot,
To make sure I understand what you’re asking, you would like to have gene expression profiles measured after a knock-down (RNAi? other method? no preference for method?) of some genes? So for example, RNA-seq of all CCLE cell lines after each cell line has had KD of gene X, then the same thing for gene Y etc.
Thx a lot for your reply and for the summary of my question. This is exactly what I’m looking for, dreaming of. I found the expression profiles for all the CCLE cell lines within the download section as well as the information about the perturbation effect in the CCLE cell lines [all or only dependent ones]. Hence, I was wondering if the expression profile of gene X [Xi -Xn] after a knock-down (no preference for the method) is also available for download.
That would be amazing, to my knowledge that data is not available (someone from DepMap can correct me if I’m wrong though, would be very pleasantly surprised!)
The only thing I know of that is somewhat related is CMap / L1000 - they use a high-throughput gene expression assay to directly measure ~1000 genes, infer the expression of ~13,000. They’ve done that in ~8-12 cell lines with ~9000 perturbagens - KD of genes, overexpression of genes, treatment with tool compounds.
Hope this helps
Too bad the data is not available, thx for confirming this. I thought maybe I just missed it. I appreciate your help and CMap recommendation. I’ll check it out.
I think this is the goal of the next stage of the DepMap project, it looks like they’re applying for funding: https://www.nature.com/articles/d41586-021-00182-0
I hope they get it, the utility of something like this would be higher than other projects like ENCODE at a fraction of the cost, and would definitely extend beyond ‘cancer biology’
What are the ways you envision yourselves and others using this type of data?
Which would be more useful for you to have first: data from genome-scale knockouts in only a few cell lines or from a limited number of KOs (~hundreds) in a set of ~100 cell lines?
PS: We have previously published post-perturbational transcriptional data (scRNA-seq) for up to 100 cell lines treated with a handful of drugs (as well as following GPX4 KO) as part of our MIX-seq study https://www.nature.com/articles/s41467-020-17440-w