The chromatin immunoprecipitation (ChIP) assay and ChIP-qPCR

Research output: Chapter in Book/Report/Conference proceedingChapter


Chromatin immunoprecipitation (ChIP) of epigenetic modifications (epiChIP) coupled with quantitative PCR (qPCR), is the current Gold Standard in epigenetic research and will continue to be so for the foreseeable future. The combination of epiChIP and qPCR seems like a match made in heaven, but in reality, it is a relationship fraught with obstacles and hidden pitfalls and generating high quality ChIP data takes time, patience and practice. This chapter aims towards outlining the history and development of ChIP-qPCR, highlight inherent challenges and illuminate pathways around obstacles by discussing the key component parts of the assay: affinity reagents, chromatin preparation, dynamic range, chromatin precipitation, qPCR and data analysis and presentation. The aim is to outline the steps needed to successfully harness the full power of the ChIP/epiChIP assay to generate reliable and reproducible results.

Original languageEnglish (US)
Title of host publicationEpigenetics Methods
Number of pages16
ISBN (Electronic)9780128194140
StatePublished - Jan 1 2020


  • ChIP
  • ChIP data analysis
  • ChIP data presentation
  • ChIP titration
  • ChIP-qPCR
  • Chromatin
  • Chromatin size distribution
  • Crosslinking
  • epiChIP
  • MNAse
  • N-ChIP
  • qPCR
  • Sonication
  • X-ChIP

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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