Where to find DNase-seq and RNA-seq assays for various cancer lines?

Question

[bhchiang]

Does anyone know where to find DNase-seq or/and RNA-seq assays of different cancer cell lines (no special treatments). I've tried looking at the SRA, but the assays I could find there are mostly studying the effects of different drugs/treatments on cancer cell lines. Thanks.

Answer 1

[jared.andrews07]

This paper has RNA-seq for 675 cancer cell lines, done by Genentech. Should be able to find whatever you need there, though you'll have to apply for access. As for the DNase, you'll have to use what's available in ENCODE or dig through the literature for your cell lines of interest.

Edit: I forgot there is also CCLE from the Broad Institute. They have a lot of RNA-seq data that you can download in RPKM or read count tables without applying for access (though you do have to register for their site).

[bhchiang]

Thanks for the answer! Do you know how long the application process typically takes or what it involves? Thanks!

[jared.andrews07]

Kind of a standard data access request - why you need the data, what you'll use it for, etc etc. I think it took us about two weeks to get access going about it in a pretty casual way. See my edit in the answer for an additional resource.