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  • 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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