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chip-seq "mock" and "control"

I have been trying to do a chip-seq analysis. I have some questions.

  1. What is "Mock" in chip-seq? This is what I understood. Mock is a sample which is immunoprecipitated, but is non-specific. Is that true?
  2. If I have a 'Control' sample and an 'experiment' sample and a "mock" sample, Do I need to run chip-seq analysis for "Mock + control" and "Mock + experiment"?
  3. Is it necessary that I should have a "Mock" while doing chip-seq? Can I run chip-seq without a mock, just with my Control and experiment sample?
chip-seq
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updated by Devon Ryan Devon Ryan • written by Rose • Rose

1 answer

  1. Typically a "mock" ChIP-seq sample is one produced using IgG or something else that's not expected to IP much of anything. The purpose of this was historically to test for regions being non-specifically IPed. In general, mock IP samples are no longer created, they turn out to not be very useful (you get almost no DNA from the IP, so you end up either getting either very few reads (problematic for normalization) and/or lots of PCR duplicates (problematic for normalization). These days people will just sequence and input sample ("control" usually).
  2. Just use control vs. experiment.
  3. Mock samples are neither required nor terribly useful; look for input/control samples and use them instead.
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written by Devon Ryan Devon Ryan

Thanks for the fast reply Devon.

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written by Rose • Rose

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