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

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Polycomb Group Proteins

Part of the book series: Methods in Molecular Biology ((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.

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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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Authors and Affiliations

  1. ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia

    Ozren Bogdanovic´

  2. Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, 6500HB, The Netherlands

    Simon J. van Heeringen

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  1. Ozren Bogdanovic´
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  2. Simon J. van Heeringen
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Correspondence to Simon J. van Heeringen .

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Editors and Affiliations

  1. IBCN-CNR, Institute of Cell Biology and Neurobiology and Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Rome, Italy

    Chiara Lanzuolo

  2. Istituto Nazionale di Genetica Molecolare “Romeo ed Enrica Invernizzi”, Milan, Italy

    Beatrice Bodega

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Bogdanovic´, O., van Heeringen, S.J. (2016). ChIP-seq Data Processing for PcG Proteins and Associated Histone Modifications. In: Lanzuolo, C., Bodega, B. (eds) Polycomb Group Proteins. Methods in Molecular Biology, vol 1480. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6380-5_4

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  • DOI: https://doi.org/10.1007/978-1-4939-6380-5_4

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6378-2

  • Online ISBN: 978-1-4939-6380-5

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