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Thread | Thread Starter | Forum | Replies | Last Post |
GO enrichment between two samples | Fernas | Bioinformatics | 4 | 05-29-2013 06:05 PM |
Sequencing low diversity samples on the MiSeq | pmiguel | Illumina/Solexa | 32 | 04-03-2013 01:47 PM |
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#1 |
Junior Member
Location: Singapore Join Date: Oct 2016
Posts: 2
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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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