title: ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications.
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.
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia.
authors.forename: Ozren
authors.initials: O
authors.lastname: Bogdanovic
authors.affiliation: Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, 6500HB, The Netherlands. s.vanheeringen@science.ru.nl.
authors.forename: Simon J
authors.initials: SJ
authors.lastname: van Heeringen
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000235:genetics*; D016678:Genome; D042421:Histone Code / Q000235:genetics; D006657:Histones / Q000235:genetics* / Q000302:isolation & purification; D063146:Polycomb-Group Proteins / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D006657:Histones; D063146:Polycomb-Group Proteins; D004247:DNA
keywords: ChIP-seq; ChIP-sequencing; H3K27me3; PRC1; PRC2; Polycomb