Question: How To Download All H3K27Me3 Chip-Seq Datsets Of Mouse At Once
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gravatar for biorepine
7.5 years ago by
biorepine1.5k
Spain
biorepine1.5k wrote:

Hi,

I know that, I can do this manually by going to either GEO or at once by going to ENCODE: ENCODE certainly does not hold all the published chromatin ChIP-Seq datasets for some unknown reason. Is there any way to extract all published ChIP-Seq datasets of any given histone mark (in my case H3K27me3) at once ?

Thanx in advance!!

mouse chip-seq • 2.5k views
ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by biorepine1.5k
2

Check this post Downloading Multi Experiment .Sra Files From Ncbi Archive Automatedly

ADD REPLYlink written 7.5 years ago by Sukhdeep Singh10k

The unknown reason is that ENCODE is not a repository for all published data - the consortium performed their own experimental data collection on specified cell lines using consistent protocols. GEO contains the ENCODE data as well as e.g. NIH Epigenomics, so GEO is the place to look.

ADD REPLYlink written 7.5 years ago by Ben2.0k
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