Chromatin Immunoprecipitation Sequencing (ChIP-seq) for Detecting Histone Modifications and Modifiers
- 30 September 2022
- book chapter
- Published by Springer Nature
- Vol. 2577, 55-64
Abstract
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the most widely used method for analyzing genome-wide DNA–protein interactions. Because there is considerable variation in the modes and strengths of DNA–protein interactions, chromatin immunoprecipitation (ChIP) protocols have been diversified and optimized for different needs. Here, we describe protocols for detecting histone modifications and modifiers using various crosslinking and immunoprecipitation conditions. We provide a complete ChIP-seq workflow covering sample preparation, immunoprecipitation, next-generation sequencing (NGS) library preparation, and data analyses. Key words Histone Immunoprecipitation Next-generation sequencing Dual crosslinkKeywords
This publication has 20 references indexed in Scilit:
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and explorationBriefings in Bioinformatics, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- FAD-dependent lysine-specific demethylase-1 regulates cellular energy expenditureNature Communications, 2012
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell IdentitiesMolecular Cell, 2010
- Fast and accurate short read alignment with Burrows–Wheeler transformBioinformatics, 2009
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology, 2009
- Model-based Analysis of ChIP-Seq (MACS)Genome Biology, 2008
- Genome-wide maps of chromatin state in pluripotent and lineage-committed cellsNature, 2007
- High-Resolution Profiling of Histone Methylations in the Human GenomeCell, 2007
- The IL-7 Receptor Controls the Accessibility of the TCRγ Locus by Stat5 and Histone AcetylationImmunity, 2001