FAIRE vs H3K27Ac ChIP
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6.0 years ago

Hi, I am using two techniques to look for open chromatin FAIRE and H3K27Ac.. I would like to send both libraries for Next-gen seq.. However, during initial q-PCR level FAIRE is giving me expected results (opening and closing of enhancer region in control vs treatment).. but H3K27Ac ChIP-qPCR is not giving me significant difference for that particular enhance in control vs treatment.. I am getting ~ 10 fold increase in signal compare to my Input which suggest that ChIP worked.. I am wondering how many time these two techniques were compared for same experimental setting? Anyone? Thanks, Ankur

 

 

ChIP-Seq genome next-gen • 1.2k views
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6.0 years ago

I don't know how a typical (if there's a typical) H3K27Ac ChIP-Seq pull down looks like. However, FAIRE and ChIP-seq are very different methods. With FAIRE you expect to retain and sequence everything that is not bound by proteins. With ChIP-Seq you sequence what is bound by your antibody (with a lot of hand-waving as these techniques are far from perfect). So I'm not that surprised by your inconsistent results, but I know nothing about your control regions...

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Thanks Dariober, my control regions are ChIP negative region for mouse genome (I am using mouse cell lines) and I don't see any enrichment in ChIPed faction for this region however some of the expected enhancers are enriched in ChIP.. 

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