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. 2009 Jul;48(3):240-8.
doi: 10.1016/j.ymeth.2009.03.001. Epub 2009 Mar 9.

ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions

Dominic Schmidt  1 , Michael D Wilson, Christiana Spyrou, Gordon D Brown, James Hadfield, Duncan T Odom
Affiliations

ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions

Dominic Schmidt et al. Methods. 2009 Jul.

Abstract

Chromatin immunoprecipitation (ChIP) allows specific protein-DNA interactions to be isolated. Combining ChIP with high-throughput sequencing reveals the DNA sequence involved in these interactions. Here, we describe how to perform ChIP-seq starting with whole tissues or cell lines, and ending with millions of short sequencing tags that can be aligned to the reference genome of the species under investigation. We also outline additional procedures to recover ChIP-chip libraries for ChIP-seq and discuss contemporary issues in data analysis.

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Figures

Figure 1
Figure 1
Outline of ChIP-seq procedure.
Figure 2
Figure 2
(A) Example whole-cell extract (WCE) sonication result. (B) Agilent Bioanalyzer 2100 traces for two ChIP-seq libraries. The left panel shows a successful library preparation. The right panel shows a library with significant amounts of adapter dimers. The quantification of the libraries is shown underneath each panel. (C) C/EBPα ChIP-seq genome track (absolute fragment count) at the albumin locus in mouse hepatocytes showing several strong and weaker binding events.
See this image and copyright information in PMC

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