Hi! I’m looking to visualize and download CRISPR dependency data from older DepMap releases. I remember that previous versions included more than one chordoma tumor cell line, but they seem to be unavailable in the most recent versions. Any help with this would be great! Thanks!
Hi,
Thanks for reaching out. If you are referring to ACH-001955, ACH-001956, and ACH-001957, their DNAseq data had been flagged and dropped in our 22Q4 release due to low quality. Since CRISPR dependency calculation relies on copy number data as an input, they have since been dropped from the dependency dataset as well.
Hope this helps!
Simone
Hi Simone, Thank you for your helpful response!
To clarify my understanding, It seems that the copy number information at the 22Q2 (last version that includes all four chordoma cell lines) was generated using WG, WES or SNP arrays. Were any of these data types flagged for low quality, leading to their removal? Or were new DNAseq data produced, and it was those that were determined to be of low quality?
I am asking because I am currently utilizing data from the 22Q2 release and I want to make sure I am doing correctly.
Thank you once again!
Dani
Hi Dani,
From what I can tell, these were flagged because of the quality of their “legacy” DNAseq profiles, and we have not regenerated omics any of these lines. Those ended up being in the 22Q2 release, so I’d recommend removing them from your analysis as well.
Best,
Simone
Thank you so much for your help, Simone!
