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Old 12-03-2012, 04:40 PM   #1
yogioner
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Location: California

Join Date: Jul 2012
Posts: 1
Default Library QC- cntrl loci enrichment doesn't match pre and post library generation

Hi all- my first post, so please be kind if I miss some expected content.

Why doesn't my post amplification enrichments match my pre amplification enrichments?

To check the quality of my recently generated libraries from ChIP, I performed qPCR on positive and negative control loci. However, the levels of enrichment no longer look like what they did on the unamplified/pre library DNA. For some the trend is correct, but not for others.

This was a well validated ChIP for histone marks.
Fragment size of IP-DNA ~200bp and library ~300bp confirmed via Bioanalyzer.
I made a library for both the input and the IP-DNA.
Pre library- I used equal vol of DNA per qPCR reaction.
Post library- I used equal concentrations of DNA per qPCR reaction.
quantification via Qubit.

Any thoughts would be appreciated. I'm not sure if people normally do this even. Thanks!
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chip-seq, chip-seq library, control loci, library generation, library qc

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