ChIP-Sequencing for low enrichment samples

warriert · 02-14-2017, 12:48 AM

Hey everyone,

So I'm pretty new here and hope to get to know you all over the period of my PhD i.e. the next 2-3 years! :P

So anyways, a lot of my current work involves preparation of ChIP-Seq libraries for a weakly bound factor i.e. a histone modifier in mouse ES cells. Now Im fairly well-versed with ChIP, its troubleshooting and optimisation. But I am still sort of a novice in terms of library preparation.

Im using the Ethanomics protocol for ChIP-Seq preparation and the trouble I have with my sample is that when I run a QC for the same using qPCR, the enrichment in terms of Input percentage is in the range of 0.05 - 0.7 %, which is quite low. We are using a Sera based antibody for our X-ChIP and the protocol for the ChIP is pretty standard.

As we have experts from the Seq world here, would anyone be willing to cast some light on how I may get optimal libraries or what conditions I can tweak to maximise my library concentration??

Cheers!

warriert

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02-14-2017, 12:48 AM	#1
warriert Junior Member Location: Singapore Join Date: Oct 2016 Posts: 2	ChIP-Sequencing for low enrichment samples Hey everyone, So I'm pretty new here and hope to get to know you all over the period of my PhD i.e. the next 2-3 years! :P So anyways, a lot of my current work involves preparation of ChIP-Seq libraries for a weakly bound factor i.e. a histone modifier in mouse ES cells. Now Im fairly well-versed with ChIP, its troubleshooting and optimisation. But I am still sort of a novice in terms of library preparation. Im using the Ethanomics protocol for ChIP-Seq preparation and the trouble I have with my sample is that when I run a QC for the same using qPCR, the enrichment in terms of Input percentage is in the range of 0.05 - 0.7 %, which is quite low. We are using a Sera based antibody for our X-ChIP and the protocol for the ChIP is pretty standard. As we have experts from the Seq world here, would anyone be willing to cast some light on how I may get optimal libraries or what conditions I can tweak to maximise my library concentration?? Cheers! warriert