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

D Schmidt, MD Wilson, C Spyrou, GD Brown… - Methods, 2009 - Elsevier
D Schmidt, MD Wilson, C Spyrou, GD Brown, J Hadfield, DT Odom
Methods, 2009Elsevier
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 …
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.
Elsevier