Question: Mouse Enhancers Database/ Mouse Enhancer annotation
1
gravatar for lucatucciarone
4 months ago by
lucatucciarone50 wrote:

Hello guys, new to the club.

I'm interested in intersecting my AcH3k27 peaks with some enhancers signature (or known enhancers) in mouse fibroblasts.

I have a couple of questions in this regard:

1) How much are enhancers signatures "Stable" across cell lines? I can understand AcH3k27 changing (Because is relative to enhancer activation) but I cannot see why Enhancers signatures should actually change between different cell lines. I am not talking about signal magnitude but the mere presence of the signature.

2) Other than H3K4me1, how can one identify and annotate enhancers? Have they been annotated? I do have a good ChIP-seq for AcH3k27 and a NA-seq for this primary mouse cells and I'm very curious to have a look at Enhancers role in my experimental settings. If you would have only this 2 dataset at hand, how would you take enhancers into consideration?

Thanks a lot;

Luca

chip-seq • 373 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by lucatucciarone50

Thank you very much! This resource will be super helpful for sure. Just a curiosity, would you think H3K27Ac is enough to describe an enhancer? Or Have it to be coupled with H3K4me1?

Thank you a lot again!

ADD REPLYlink written 4 months ago by lucatucciarone50

According to this reference: http://www.statehub.org, H3K4me1 is related to the regulatory function whereas H3K27ac is related to level of activity.

ADD REPLYlink written 4 months ago by jomo018470
0
gravatar for jomo018
4 months ago by
jomo018470
jomo018470 wrote:

For enhancer list, consider http://www.enhanceratlas.org/download2.php. Click download enhancers and scroll to mouse tissue for Fibroblast.

On page http://www.enhanceratlas.org/index2.php you can find a short description of their method along with a reference.

ADD COMMENTlink modified 4 months ago • written 4 months ago by jomo018470
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: 2172 users visited in the last hour