Question: chip-seq "mock" and "control"
0
gravatar for Rose
4 weeks ago by
Rose0
Rose0 wrote:

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 • 180 views
ADD COMMENTlink modified 4 weeks ago by Devon Ryan74k • written 4 weeks ago by Rose0
2
gravatar for Devon Ryan
4 weeks ago by
Devon Ryan74k
Freiburg, Germany
Devon Ryan74k wrote:
  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.
ADD COMMENTlink written 4 weeks ago by Devon Ryan74k

Thanks for the fast reply Devon.

ADD REPLYlink written 4 weeks ago by Rose0
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