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.
Highlights
Chromatin immunoprecipitation (ChIP)-seq is one of several recently introduced high-throughput chromatin profiling assays based on next-generation sequencing (NGS) technology [1]
The principles for analyzing the data obtained with these techniques are similar, though specialized computer programs have been developed in different application areas
We present an introduction into the principles of ChIP-seq data analysis in form of a tutorial which uses tools from the ChIP-Seq servera and the Signal Search Analysis (SSA) server [3], two bioinformatics resources maintained by our group
Summary
ChIP-seq is one of several recently introduced high-throughput chromatin profiling assays based on next-generation sequencing (NGS) technology [1]. The input data file contains the chromosomal coordinates of the 5’ ends of the fragments as determined by mapping the sequence reads from the STAT1 ChIP-seq experiment to the genome. Genome: H. sapiens (March 2006/hg18) Data type: ChIP-seq Series: Robertson 2007 Sample: Hela-S3 STAT1 INFg Additional Input Data Options
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