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Evaluation of 3D Chromatin Interactions Using Hi-C

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Stem Cell Transcriptional Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2117))

Abstract

The invention of Hi-C has greatly facilitated 3D genome research through an unbiased probing of 3D chromatin interactions. It produces enormous amount of sequencing data that capture multiscale chromatin conformation structures. In the last decade, numerous computational methods have been developed to analyze Hi-C data and predict A/B compartments, topologically associating domains (TADs), and significant chromatin contacts. This chapter introduced the iHiC package that provides several utilities to facilitate Hi-C data analysis with public software and demonstrated its application to a Hi-C dataset generated for mouse embryonic stem (ES) cells.

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Acknowledgments

The author thanks Dr. Xiaobin Zheng from Carnegie Institution for Science and Mr. Aniello Infante in the lab for helpful comments. The work was partially supported by National Institute of General Medical Sciences Grant 5U54GM104942-04.

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Authors and Affiliations

  1. Department of Microbiology, Immunology, and Cell Biology, West Virginia University School of Medicine, Morgantown, WV, USA

    Gangqing Hu

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  1. Gangqing Hu
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Correspondence to Gangqing Hu .

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Editors and Affiliations

  1. Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA

    Benjamin L. Kidder

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Hu, G. (2020). Evaluation of 3D Chromatin Interactions Using Hi-C. In: Kidder, B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, vol 2117. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0301-7_3

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  • DOI: https://doi.org/10.1007/978-1-0716-0301-7_3

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0300-0

  • Online ISBN: 978-1-0716-0301-7

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