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Tiling Arrays pp 51–64Cite as

Genome-Wide Analysis of Transcription Factor-Binding Sites in Skeletal Muscle Cells Using ChIP-Seq

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1067))

Abstract

Transcriptional regulation of gene expression constitutes a fundamental mechanism of many developmental processes. Therefore, identification and characterization of binding sites of transcription factors are important for uncovering the mechanisms of a particular developmental process. Here, we describe detailed procedures for genome-wide analysis of binding sites of a transcription factor involved in the fiber-type differentiation of skeletal muscle. By conducting ChIP-seq followed by a series of downstream analyses, in-depth information on binding sites of transcription factors can be obtained in a genome-wide manner.

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Acknowledgments

We thank Mr. Adam Jenkins for helpful discussions and Dr. Charles Nicolet at the DNA Technologies and Expression Analysis Core Facilities of the UC Davis Genome Center for assistance with the ChIP-seq experiments. This work was supported by Expression Analysis Core Seed Grant, Muscular Dystrophy Association (MDA 4135), and the National Institutes of Health (AR055209) (to N.H.).

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Authors and Affiliations

  1. Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, Davis, CA, USA

    Chung-II An & Nobuko Hagiwara

Authors
  1. Chung-II An
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  2. Nobuko Hagiwara
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Editor information

Editors and Affiliations

  1. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

    Tin-Lap Lee

  2. Rm 624A Area 39, The Chinese University of Hong Kong Reproduction, Development and Endocrinol, Hong Kong, China, People's Republic

    Alfred Chun Shui Luk

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An, CI., Hagiwara, N. (2013). Genome-Wide Analysis of Transcription Factor-Binding Sites in Skeletal Muscle Cells Using ChIP-Seq. In: Lee, TL., Shui Luk, A. (eds) Tiling Arrays. Methods in Molecular Biology, vol 1067. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-607-8_4

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  • DOI: https://doi.org/10.1007/978-1-62703-607-8_4

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-606-1

  • Online ISBN: 978-1-62703-607-8

  • eBook Packages: Springer Protocols

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