ChIP-Seq: technical considerations for obtaining high-quality data

Nat Immunol. 2011 Sep 20;12(10):918-22. doi: 10.1038/ni.2117.


Chromatin immunoprecipitation followed by next-generation sequencing analysis (ChIP-Seq) is a powerful method with which to investigate the genome-wide distribution of chromatin-binding proteins and histone modifications in any genome with a known sequence. The application of this technique to a variety of developmental and differentiation systems has provided global views of the cis-regulatory elements, transcription factor function and epigenetic processes involved in the control of gene transcription. Here we describe several technical aspects of the ChIP-Seq assay that diminish bias and background noise and allow the consistent generation of high-quality data.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Animals
  • Antibodies, Monoclonal / immunology
  • Cell Count
  • Chromatin
  • Chromatin Immunoprecipitation / methods*
  • Gene Library
  • Mice
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Statistics as Topic


  • Antibodies, Monoclonal
  • Chromatin