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Does anyone have any ideas on how to run a control/input sample for a ChIP-exo experiment? Is it even necessary to run a control (similar to input DNA for ChIP-seq)? I'm looking for any references or forums that discuss this issue and experimental design?

This video (https://www.youtube.com/watch?v=8qLRI9Bqtso) briefly touches on this issue (t=32.45), indicating NOT to use an Input sample due to the Exo digestion. However, I don't know how the community (or reviewers) feel about this?

Thanks for any help!

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  • $\begingroup$ There is a recently published paper addressing the lack of input controls for ChIP-Exo procedures. doi.org/10.1093/nar/gkw741 Hope this helps $\endgroup$ – Nate S. Mar 1 '17 at 21:32

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