ChIP-Seq: Library Preparation and Sequencing

Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) has been used extensively to determine the genome-wide location of DNA-binding factors, such as transcription factors, posttranscriptionally modified histones, and members of the transcription complex, to assess regulatory input, epigenetic modifications, and transcriptional activity, respectively. Here we describe methods to isolate chromatin from tissues, immunoprecipitate DNA bound to a protein of interest, and perform next-generation sequencing to identify a genome-wide DNA-binding pattern.