I want to download histone modifications and transcription factor binding sites data from ENCODE.
In this link below: https://www.encodeproject.org/matrix/?type=Experiment&status=released
There are tissues and cell lines, from which of them I should download data?
Thanks, Burcak
Cell lines are usually derived from cancerous cells. The ENCODE samples from tissues represent tissues taken from deceased donors (in the case of human data) or wildtype Bl6 mice. I.e. the tissues are probably as close to "healthy" or "normal" tissue as you can get.
Yes, I think so. When I search for some cell lines in https://www.atcc.org/ they came out to be all cancer cell lines. But tissues seem to be from normal donors. But, of course I could not do this verification for all. Thanks.
If the origin of the cells is of great importance, you'll definitely have to double check with the actual lab that generated the data. ENCODE is the parent organization for numerous individual labs/grants, and some specialized assays, e.g. ATAC-seq, may be performed on different types of, say, liver tissue, than the "corresponding" RNA-seq.
You can glean many technical details about some of the individual RNA-seq samples from this paper
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That'll depend on the overall goal of your analysis. For example, if you would like to compare the ENCODE results with some results you or a collaborator have obtained from, say, K562 cells, then it would probably make sense to download those.
What I have is cancer tissues across many tissues. But I do not know whether tissues in ENCODE come from normal tissues or cancer tissues.