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AAT Bioquest

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 validated for ChIP applications, or use one validated for immunoprecipitation (IP)
  3. Optimize the antibody-to-chromatin ratio for efficient immunoprecipitation. 
  4. Use polyclonal antibodies or epitope tags to reduce false negatives. 
  5. Use the right chromatin preparation method based on the target proteins, such as xChIP for weak DNA binding. 
  6. Confirm chromatin fragmentation using agarose gel electrophoresis after DNA purification. 
  7. Compare protein enrichment of target sequences to unrelated regions to validate results. 
  8. Preserve post-translational modifications with 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.
Additional resources

Chromatin Immunoprecipitation Assay as a Tool for Analyzing Transcription Factor Activity

Chromatin Immunoprecipitation (ChIP)

ReadiPrep™ Protein A-Agarose Resin

Antibody & Protein Conjugation Service