How To Download All H3K27Me3 Chip-Seq Datsets Of Mouse At Once

Question

[biorepine]

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!!

[Sukhi Singh]

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

[Ben]

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.