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Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

Author

Listed:
  • Wenfei Jin

    (Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health)

  • Qingsong Tang

    (Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health)

  • Mimi Wan

    (Yale University School of Medicine)

  • Kairong Cui

    (Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health)

  • Yi Zhang

    (Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health
    Institute of Immunology, Third Military Medical University of the People’s Liberation Army)

  • Gang Ren

    (Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health
    College of Animal Science and Technology, Northwest A&F University)

  • Bing Ni

    (Institute of Immunology, Third Military Medical University of the People’s Liberation Army)

  • Jeffrey Sklar

    (Yale University School of Medicine)

  • Teresa M. Przytycka

    (Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health)

  • Richard Childs

    (Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health)

  • David Levens

    (Laboratory of Pathology, National Cancer Institute, National Institutes of Health)

  • Keji Zhao

    (Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health)

Abstract

A DNase sequencing method termed scDNase-seq detects DNase I hypersensitive sites genome-wide in single cells and pools of cells dissected from cancer biopsies.

Suggested Citation

  • Wenfei Jin & Qingsong Tang & Mimi Wan & Kairong Cui & Yi Zhang & Gang Ren & Bing Ni & Jeffrey Sklar & Teresa M. Przytycka & Richard Childs & David Levens & Keji Zhao, 2015. "Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples," Nature, Nature, vol. 528(7580), pages 142-146, December.
    • Handle: RePEc:nat:nature:v:528:y:2015:i:7580:d:10.1038_nature15740
    DOI: 10.1038/nature15740
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    Cited by:

    1. Qiang Shan & Xiang Li & Xia Chen & Zhouhao Zeng & Shaoqi Zhu & Kexin Gai & Weiqun Peng & Hai-Hui Xue, 2021. "Tcf1 and Lef1 provide constant supervision to mature CD8+ T cell identity and function by organizing genomic architecture," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
    2. Steven Henikoff & Jorja G. Henikoff & Kami Ahmad & Ronald M. Paranal & Derek H. Janssens & Zachary R. Russell & Frank Szulzewsky & Sita Kugel & Eric C. Holland, 2023. "Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    3. Youtao Lu & Jaehee Lee & Jifen Li & Srinivasa Rao Allu & Jinhui Wang & HyunBum Kim & Kevin L. Bullaughey & Stephen A. Fisher & C. Erik Nordgren & Jean G. Rosario & Stewart A. Anderson & Alexandra V. U, 2023. "CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    4. Sang-A Park & Yun-Ji Lim & Wai Lim Ku & Dunfang Zhang & Kairong Cui & Liu-Ya Tang & Cheryl Chia & Peter Zanvit & Zuojia Chen & Wenwen Jin & Dandan Wang & Junji Xu & Ousheng Liu & Fu Wang & Alexander C, 2022. "Opposing functions of circadian protein DBP and atypical E2F family E2F8 in anti-tumor Th9 cell differentiation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Gang Ren & Wai Lim Ku & Guangzhe Ge & Jackson A. Hoffman & Jee Youn Kang & Qingsong Tang & Kairong Cui & Yong He & Yukun Guan & Bin Gao & Chengyu Liu & Trevor K. Archer & Keji Zhao, 2024. "Acute depletion of BRG1 reveals its primary function as an activator of transcription," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    6. Alan Yue Yang Teo & Jordan W. Squair & Gregoire Courtine & Michael A. Skinnider, 2024. "Best practices for differential accessibility analysis in single-cell epigenomics," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

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