I am a beginner in performing Chromatin Immunoprecipitation. While reading manuals and notes on ChIP and its data analysis , I came across two main methods of interpretation of ones results: Percent Input method and Fold enrichment method. While one uses Input chromatin as the reference sample, the other uses the mock IgG as the reference. Can experts please elaborate on the advantages and disadvantages of both the methods and suggest which one I should adopt?
Thanks
this link is useful
https://www.thermofisher.com/mx/en/...chip/chip-analysis.html
regards
Thank you Dr. Hassan Nima. I was referring to this document too but was unclear about the advantage of using Input to normalise IP fraction over IgG.
Deare Antara
ChIP-qPCR data needs to be normalized for sources of variability, including amount of chromatin, efficiency of immunoprecipitation, and DNA recovery. Two common methods used to normalize ChIP-qPCR data—the Percent Input Method and the Fold Enrichment Method. We prefer analyzing ChIP-qPCR data relative to input as this includes normalization for both background levels and input chromatin going into the ChIP. We recommend that ChIP experiments are run in replicate and that the results are presented together with the background signal and standard error when possible. Best and kind regard
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