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What should I consider in order to get the best chromatin immunoprecipitation (ChIP) results in my experiment?
Posted April 12, 2024

Answer

There are several factors one should consider in order to get the best ChIP results in their experiment. 

  1. Use an appropriate control, like an isotype control or non-related antibody, to assess antibody specificity.
  2. Ensure that the antibody is validatedfor ChIP applications, or use one validated for immunoprecipitation (IP)
  3. Optimize the antibody-to-chromatin ratiofor efficient immunoprecipitation. 
  4. Use polyclonal antibodies or epitope tagsto reduce false negatives. 
  5. Use the right chromatin preparation methodbased on the target proteins, such as xChIP for weak DNA binding. 
  6. Confirm chromatin fragmentationusing agarose gel electrophoresis after DNA purification. 
  7. Compare protein enrichment of target sequencesto unrelated regions to validate results. 
  8. Preserve post-translational modificationswith specific inhibitors to stop degradation of the modifications on proteins. 
  9. Verify  ChIP DNA quality(at a minimum of 5-fold enrichment) through PCR or qPCR, comparing them to controls.