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Genome-Wide Analysis of DNA Methylation in Single Cells Using a Post-bisulfite Adapter Tagging Approach

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Next Generation Sequencing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1712))

Abstract

DNA methylation is an epigenetic mark implicated in the regulation of key biological processes. Using high-throughput sequencing technologies and bisulfite-based approaches, it is possible to obtain comprehensive genome-wide maps of the mammalian DNA methylation landscape with a single-nucleotide resolution and absolute quantification. However, these methods were only applicable to bulk populations of cells. Here, we present a protocol to perform whole-genome bisulfite sequencing on single cells (scBS-Seq) using a post-bisulfite adapter tagging approach. In this method, bisulfite treatment is performed prior to library generation in order to both convert unmethylated cytosines and fragment DNA to an appropriate size. Then DNA fragments are pre-amplified with concomitant integration of the sequencing adapters, and libraries are subsequently amplified and indexed by PCR. Using scBS-Seq we can accurately measure DNA methylation at up to 50% of individual CpG sites and 70% of CpG islands.

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Author information

Authors and Affiliations

  1. Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK

    Heather J. Lee

  2. School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, 2308, NSW, Australia

    Heather J. Lee

  3. Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058, Basel, Switzerland

    Sébastien A. Smallwood

  4. Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK

    Sébastien A. Smallwood

Authors
  1. Heather J. Lee
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  2. Sébastien A. Smallwood
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Corresponding authors

Correspondence to Heather J. Lee or Sébastien A. Smallwood .

Editor information

Editors and Affiliations

  1. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, USA

    Steven R. Head

  2. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, USA

    Phillip Ordoukhanian

  3. Department of Molecular Medicine, The Scripps Research Institute Center for Organ and Cell Transplantation, La Jolla, California, USA

    Daniel R. Salomon

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Lee, H.J., Smallwood, S.A. (2018). Genome-Wide Analysis of DNA Methylation in Single Cells Using a Post-bisulfite Adapter Tagging Approach. In: Head, S., Ordoukhanian, P., Salomon, D. (eds) Next Generation Sequencing. Methods in Molecular Biology, vol 1712. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7514-3_7

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  • DOI: https://doi.org/10.1007/978-1-4939-7514-3_7

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7512-9

  • Online ISBN: 978-1-4939-7514-3

  • eBook Packages: Springer Protocols

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