Chip-seq Binding sites

Question

[atsalaki]

Where can i find chip-seq peak files except ENCODE for various Transcription factors in various cell lines(e.g. i am looking CTCF with MCF7 binding sites)? Iam looking for files with hundreds or thousands of genes.

[natasha.sernova]

See these articles:

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2940-7

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-80

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

http://tools.thermofisher.com/content/sfs/brochures/ChipSeq-Application-Note-CO28266.pdf

but note,

"Genomic binding sites for CTCF, H3K27ac, and H3K27me3 identified in K-562 cells using the MAGnify ™ Chromatin Immunoprecipitation System and the Ion Proton ™ System were compared to ENCODE project results "

Answer 1

[Denise CS]

Check the Ensembl Regulatory Build. You will find Roadmap and Blueprint there, besides ENCODE. Check one of the Ensembl blog posts on the addition of Blueprint data.