Ambrosini, GiovannaDreos, ReneBucher, Philipp2015-02-202015-02-202015-02-202014https://infoscience.epfl.ch/handle/20.500.14299/111184WOS:000346381500076Chromatin immunoprecipitation (ChIP) followed by high-throughput 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 ChIP-seq 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-seqDNase I hypersensitive sitestranscription factor binding siteshistone marksbioinformatics analysistext::conference output::conference proceedings::conference paper