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
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