ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1480)

Abstract

Chromatin Immunoprecipitation followed by massively parallel DNA sequencing (ChIP-sequencing) has emerged as an essential technique to study the genome-wide location of DNA- or chromatin-associated proteins, such as the Polycomb group (PcG) proteins. After being generated by the sequencer, raw ChIP-seq sequence reads need to be processed by a data analysis pipeline. Here we describe the computational steps required to process PcG ChIP-seq data, including alignment, peak calling, and downstream analysis.

Key words

Polycomb ChIP-seq ChIP-sequencing PRC1 PRC2 H3K27me3 

Notes

Acknowledgments

O.B. is supported by an Australian Research Council Discovery Early Career Researcher Award—DECRA (DE140101962); S.J.v.H. is supported by the Netherlands Organization for Scientific Research (NWO-ALW grant 863.12.002).

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthAustralia
  2. 2.Radboud University, Department of Molecular Developmental Biology, Faculty of ScienceRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands

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