The miRNA data in GeCKO screen

Q&A
,
1

The Human GeCKO v2 library also includes 7456 guide RNAs targeting 1864 miRNAs. However, I can’t find it in the data file downloaded from DepMap. Can I access the RAW FASTQ files to extract those data by ourselves? Thank you very much.

Best,
Larry

2

Hi Larry,

The GeCKO data and library annotations are here: DepMap GeCKO 19Q1

3

Hi Joshua,

Thank you for your reply. I checked all the files from GeCKO data and library annotations before, they don’t contain the miRNA data. In Feng’s paper for human GeCKO v2 screening ( [Sanjana et al Nat Methods. 2014 Aug;11(8):783-4. doi: 10.1038/nmeth.3047], the human GeCKO v2 library contains 122,411 guide RNAs targeting 19,050 genes and 1,864 miRNAs, but in DepMap’s GeCKO data, I can only find the data for 19,050 genes but not miRNAs.

4

Hi Lai,

I’m afraid access to the FASTQ files isn’t something we currently offer.