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Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions

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Enhancers and Promoters

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2351))

Abstract

The open chromatin enrichment and network Hi-C (OCEAN-C) was developed not only for identifying large-scale chromatin structures, including topologically associated domains (TADs) and A/B compartments, but also for globally mapping hubs of open chromatin interactions (HOCIs) and their interaction networks independent of antibody and bait-sequences.

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Acknowledgments

This work was supported by National Natural Science Foundation of China (31871266). Part of the data analysis was performed on the High Performance Computing Platform of the Center for Life Sciences, Peking University. We thank Zhihua Zhang for providing the GM12878 cell line, and Yong Cao for performing the experiments. We want to thank Qing Chen, Yujie Sun, Xiong Ji, Yong Zhang, Zhihua Zhang, and Yixin Yao for critical comments on this study.

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Authors and Affiliations

  1. Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing, China

    Lumeng Jia & Cheng Li

  2. State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing, China

    Tingting Li

Authors
  1. Lumeng Jia
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  2. Cheng Li
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  3. Tingting Li
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Corresponding authors

Correspondence to Cheng Li or Tingting Li .

Editor information

Editors and Affiliations

  1. Institute of Biochemistry, University of Giessen, Gießen, Hessen, Germany

    Tilman Borggrefe

  2. Institute of Biochemistry, University of Giessen, Gießen, Hessen, Germany

    Benedetto Daniele Giaimo

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© 2021 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Jia, L., Li, C., Li, T. (2021). Using Open Chromatin Enrichment and Network Hi-C (OCEAN-C) to Identify Open Chromatin Interactions. In: Borggrefe, T., Giaimo, B.D. (eds) Enhancers and Promoters. Methods in Molecular Biology, vol 2351. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1597-3_12

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  • DOI: https://doi.org/10.1007/978-1-0716-1597-3_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1596-6

  • Online ISBN: 978-1-0716-1597-3

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