Question: Chip-seq data and Hi C data
0
gravatar for tarek.mohamed
2.8 years ago by
tarek.mohamed260
tarek.mohamed260 wrote:

Dear All,

I have analyzed a chip-seq data from which I identified a peak that is located about 10 kb upstream of an interesting gene. I want to see if this binding site is located in an enhancer region. How can I use Hi-C data to confirm this distal binding site?

Thanks Tarek

chip-seq hi-c • 1.2k views
ADD COMMENTlink modified 2.8 years ago by igor9.5k • written 2.8 years ago by tarek.mohamed260
0
gravatar for igor
2.8 years ago by
igor9.5k
United States
igor9.5k wrote:

I want to see if this binding site is located in an enhancer region.

To see if it's an enhancer region, you need to have at least H3K27ac ChIP-seq data.

How can I use Hi-C data to confirm this distal binding site?

Are you trying to see if that site interacts with the gene? When you do Hi-C, you should end up with an interaction matrix that will have interactions for all regions against all others. You just need to look up the region of interest. However, most Hi-C is done at 40kb resolution. Even if you find high-quality 10kb resolution Hi-C, that is still way too coarse in your case.

ADD COMMENTlink written 2.8 years ago by igor9.5k

Hi Igor,

Thank you for your reply. My chip-seq experiment was done using human heart samples, so I have to use HI-C data from the same tissue type. I am not familiar with Hi C data sets. Is there a database where I can pull down an experiment that fits my chip-seq? Also, what software/package do you recommend for such analysis. My chip-seq was analyzed as follows, FASTQ files were aligned to GRCh38 using bowtie , Peaks were called using MACS2, ChIPseek package and R to annotate the peaks.

Thanks Tarek

ADD REPLYlink written 2.8 years ago by tarek.mohamed260

WashU EpiGenome Browser has some public datasets already loaded: http://epigenomegateway.wustl.edu/browser/

That's probably the easiest place to start.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by igor9.5k
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: 1676 users visited in the last hour