Question: Chip-seq Binding sites
1
gravatar for atsalaki
3.2 years ago by
atsalaki10
atsalaki10 wrote:

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.

binding-sites chip-seq • 1.1k views
ADD COMMENTlink modified 3.2 years ago by Denise - Open Targets5.0k • written 3.2 years ago by atsalaki10
1

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 "

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by natasha.sernova3.7k
3
gravatar for Denise - Open Targets
3.2 years ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

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.

ADD COMMENTlink written 3.2 years ago by Denise - Open Targets5.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1664 users visited in the last hour