Principles of ChIP-seq Data Analysis Illustrated with Examples

  • Giovanna Ambrosini EPFL École polytechnique fédérale de Lausanne
  • René Dreos Swiss Institute of Bioinformatics
  • Philipp Bucher EPFL École polytechnique fédérale de Lausanne

Abstract

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.

Published
2015-09-18
How to Cite
AMBROSINI, Giovanna; DREOS, René; BUCHER, Philipp. Principles of ChIP-seq Data Analysis Illustrated with Examples. Genomics and Computational Biology, [S.l.], v. 1, n. 1, p. e22, sep. 2015. ISSN 2365-7154. Available at: <https://genomicscomputbiol.org/ojs3/GCB/article/view/36>. Date accessed: 25 june 2019. doi: https://doi.org/10.18547/gcb.2015.vol1.iss1.e22.
Section
Analytical Workflows