Where to find RNAseq data

I was wondering if there is RNAseq data available for the CRISPR KO cell lines?
If yes, where can I find that data?

Thank you!

Are you asking where to find the expression data for cell lines after they’ve had a gene knocked out? If so, no, we don’t have that data, we only collect the expression of the pre-perturbed line.

However, you can find the pre-perturbed line’s expression data in the portal or download it from https://depmap.org/portal/download/


Thank you Phil,

yes this was what I was looking for

Hi Phil,

I wonder if there are RNA-Seq fastq/bam files available for downloading for all the cell lines?


I believe the raw RNA sequencing data has the same issues as the DNA sequencing data which has slowed it’s release.

The original CCLE collection did have their BAM files released, however, for new lines (about 400) we are still figuring out a path to release these BAM files in a manner that complies with patient privacy and MTAs.

For information about the CCLE released sequencing data, see this post: Accessing raw sequencing data