CRISPR screen and RNA-seq

Q&A
1

Hi,

Do CRISPR screens have whole-transcriptome RNA-seq data (bulk or single-cell) associated to them? How can I extract high level study information containing cell line, type of genetic manipulation and RNA-seq technology

Thanks

M

2

No, the CRISPR is from a pooled CRISPR knockout experiment, where the readout is cell viability per knockout. There is no post-perturbation expression data collected.

In the DepMap portal, we do have expression data, but that was measured in the absence of any perturbation. All expression data in the DepMap portal today is basal expression.

Thanks,
Phil

3

Many thanks Phil!