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Robust single-cell DNA methylome profiling with snmC-seq2

Author

Listed:
  • Chongyuan Luo

    (The Salk Institute for Biological Studies
    The Salk Institute for Biological Studies)

  • Angeline Rivkin

    (The Salk Institute for Biological Studies)

  • Jingtian Zhou

    (The Salk Institute for Biological Studies)

  • Justin P. Sandoval

    (The Salk Institute for Biological Studies)

  • Laurie Kurihara

    (Swift Biosciences Inc.)

  • Jacinta Lucero

    (The Salk Institute for Biological Studies)

  • Rosa Castanon

    (The Salk Institute for Biological Studies)

  • Joseph R. Nery

    (The Salk Institute for Biological Studies)

  • António Pinto-Duarte

    (The Salk Institute for Biological Studies)

  • Brian Bui

    (The Salk Institute for Biological Studies)

  • Conor Fitzpatrick

    (The Salk Institute for Biological Studies)

  • Carolyn O’Connor

    (The Salk Institute for Biological Studies)

  • Seth Ruga

    (Zymo Research Corporation)

  • Marc E. Van Eden

    (Zymo Research Corporation)

  • David A. Davis

    (University of Miami)

  • Deborah C. Mash

    (University of Miami)

  • M. Margarita Behrens

    (The Salk Institute for Biological Studies)

  • Joseph R. Ecker

    (The Salk Institute for Biological Studies
    The Salk Institute for Biological Studies)

Abstract

Single-cell DNA methylome profiling has enabled the study of epigenomic heterogeneity in complex tissues and during cellular reprogramming. However, broader applications of the method have been impeded by the modest quality of sequencing libraries. Here we report snmC-seq2, which provides improved read mapping, reduced artifactual reads, enhanced throughput, as well as increased library complexity and coverage uniformity compared to snmC-seq. snmC-seq2 is an efficient strategy suited for large-scale single-cell epigenomic studies.

Suggested Citation

  • Chongyuan Luo & Angeline Rivkin & Jingtian Zhou & Justin P. Sandoval & Laurie Kurihara & Jacinta Lucero & Rosa Castanon & Joseph R. Nery & António Pinto-Duarte & Brian Bui & Conor Fitzpatrick & Caroly, 2018. "Robust single-cell DNA methylome profiling with snmC-seq2," Nature Communications, Nature, vol. 9(1), pages 1-6, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-06355-2
    DOI: 10.1038/s41467-018-06355-2
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    Cited by:

    1. Jingyang Qian & Jie Liao & Ziqi Liu & Ying Chi & Yin Fang & Yanrong Zheng & Xin Shao & Bingqi Liu & Yongjin Cui & Wenbo Guo & Yining Hu & Hudong Bao & Penghui Yang & Qian Chen & Mingxiao Li & Bing Zha, 2023. "Reconstruction of the cell pseudo-space from single-cell RNA sequencing data with scSpace," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    2. Ruth V. Nichols & Brendan L. O’Connell & Ryan M. Mulqueen & Jerushah Thomas & Ashley R. Woodfin & Sonia Acharya & Gail Mandel & Dmitry Pokholok & Frank J. Steemers & Andrew C. Adey, 2022. "High-throughput robust single-cell DNA methylation profiling with sciMETv2," Nature Communications, Nature, vol. 13(1), pages 1-10, December.

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