Is it possible to download in bulk, mRNA expression levels (e.g. from the Expression 22Q1 Public dataset) only for a selction of cell lines of my choosing?

Q&A
1

I would need to obtain mRNA expression levels of certain proteins only for particular cell lines (that we have available in the lab). Up until now I am using the Expression 22Q1 public dataset and I export in excel format the mRNA levels of e.g. gene A in all cell lines available on DepMap. Is it possible to only download the mRNA levels of the cell lines I am interested in?

2

Hi. No. I’d use the same subsetting procedure that you described. You can select the cell lines that you’re interested in based on the rows with different arxspan IDs. Otherwise, we don’t provide data separated per cell line.

3

Thank you very much for your reply!

Follow-up question: is it possible to download mRNA levels for more than two genes in the same excel file?

4

Hi, we only provide the full matrix of cell lines versus genes/transcripts, so any further subsetting should be done by the user, We don’t provide custom subsetted files for download.