shRNA and sgRNA sequences

Q&A
1

Hi Depmap team,

I was wondering if there is any downloadable list or information regarding the shRNA sequences used (or even sgRNA) in the datasets?

Thanks!

1 Like
2

For both the RNAi and the CRISPR datasets the Achilles project generated, we provide the shRNA and sgRNA sequences as a download.

For example: DepMap Data Downloads contains
Achilles_guide_map.csv which contains the sequences for the sgRNAs among a few other columns.

For the RNAi data, DepMap Data Downloads contains D2_combined_hp_data.csv which has a column for the shRNA sequences.

Thanks,
Phil

3

Hi Phil,

Thanks a lot, that’s very helpful!! I just downloaded the shRNA sequences table. Is there an easy way for me to find the shRNA for my gene of interest? the table doesn’t contain Gene ID information :slight_smile:

Cheers

L

4

The shRNA → gene mapping is contained in shRNA-mapping.csv in the same DEMETER 2 release.

Thanks,
Phil