Question: What is the difference between tissues and cell lines in ENCODE>
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gravatar for burcakotlu
5 months ago by
burcakotlu40
Turkey
burcakotlu40 wrote:

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

encode cell line • 184 views
ADD COMMENTlink written 5 months ago by burcakotlu40
1

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.

ADD REPLYlink written 5 months ago by Friederike5.3k

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.

ADD REPLYlink written 5 months ago by burcakotlu40
1
gravatar for Friederike
5 months ago by
Friederike5.3k
United States
Friederike5.3k wrote:

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.

ADD COMMENTlink written 5 months ago by Friederike5.3k

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.

ADD REPLYlink written 5 months ago by burcakotlu40

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

ADD REPLYlink written 5 months ago by Friederike5.3k
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