Principles of ChIP-seq Data Analysis Illustrated with Examples

Giovanna Ambrosini, René Dreos, Philipp Bucher

GCB, Vol. 1, No. 1 (2015): e22


Chromatin immunoprecipitation (ChIP) followed by highthroughput sequencing (ChIP-seq) is a powerful method to determine how transcription factors and other chromatin-associated proteins interact with DNA in order to regulate gene transcription. A single ChIPseq experiment produces large amounts of highly reproducible data. The challenge is to extract knowledge from the data by thoughtful application of appropriate bioinformatics tools. Here we present a concise introduction into ChIP-seq data analysis in the form of a tutorial based on tools developed by our group. We expose biological questions, explain methods and provide guidelines for the interpretation of the results. While this article focuses on ChIP-seq, most of the algorithms and tools we present are applicable to other chromatin profiling assays based on next generation sequencing (NGS) technology as well.


ChIP-seq, DNase I hypersensitive sites, transcription factor binding sites, histone marks, bioinformatics analysis

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Copyright (c) 2015 Giovanna Ambrosini, René Dreos, Philipp Bucher

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This work is licensed under a Creative Commons Attribution 4.0 International License.