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ChIP Input (control) necessity - (Oct/15/2008 )

We are doing a ChIP_seq experiment looking at methylation between treated mice
and non-treated control mice using deep-sequencing methods. Please explain to me the necessity or non-
necessity of running the input or supernatant samples when comparing the treated
mice samples and the control mice samples. Why would the input samples be


You need to compare how efficient your IP works. Ideally, your IP target DNA would be > 1% of your input DNA target to indicate a successful IP.

You also need to show equal amount of input chromatin DNA, or if not equal, then use input DNA to determine target gene fold differences between two mice.

Good luck