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Chromatin Immunoprecipitation and High-Throughput Sequencing (ChIP-Seq): Tips and Tricks Regarding the Laboratory Protocol and Initial Downstream Data Analysis

  • Darren K. Patten
  • Giacomo Corleone
  • Luca MagnaniEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1767)

Abstract

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become an essential tool for epigenetic scientists. ChIP-seq is used to map protein-DNA interactions and epigenetic marks such as histone modifications at the genome-wide level. Here we describe a complete ChIP-seq laboratory protocol (tailored toward processing tissue samples as well as cell lines) and the bioinformatic pipelines utilized for handling raw sequencing files through to peak calling.

Keywords

Chromatin immunoprecipitation and high-throughput sequencing ChIP-seq Antibodies DNA library assembly ChIP-seq data processing Bioinformatics Bioinformatic pipelines Genome alignment Peak calling 

Notes

Acknowledgement

This work was supported by the European Union Horizon 2020 research and innovation programme (642691).

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Darren K. Patten
    • 1
    • 2
  • Giacomo Corleone
    • 1
  • Luca Magnani
    • 1
    Email author
  1. 1.Department of Surgery and CancerImperial College LondonLondonUK
  2. 2.Department of Bariatric and Emergency General SurgeryHomerton University HospitalLondonUK

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