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Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

Nature Methods volume 11, pages 817820 (2014) | Download Citation

Abstract

We report a single-cell bisulfite sequencing (scBS-seq) method that can be used to accurately measure DNA methylation at up to 48.4% of CpG sites. Embryonic stem cells grown in serum or in 2i medium displayed epigenetic heterogeneity, with '2i-like' cells present in serum culture. Integration of 12 individual mouse oocyte datasets largely recapitulated the whole DNA methylome, which makes scBS-seq a versatile tool to explore DNA methylation in rare cells and heterogeneous populations.

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Gene Expression Omnibus

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Sequence Read Archive

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Acknowledgements

We thank K. Tabbada and the Welcome Trust Sanger Institute sequencing pipeline team for assistance with Illumina sequencing, R. Walker for assistance with flow cytometry, T. Hore (Babraham Institute, Cambridge, UK) for providing ESCs maintained in 2i medium and serum conditions, and T. Hore, J. Huang, I. Macaulay, S. Lorenz, M. Quail, T. Voet and H. Swerdlow for helpful discussions. This work was supported by the UK Biotechnology and Biological Sciences Research Council grant BB/J004499/1, UK Medical Research Council grant MR/K011332/1, Wellcome Trust award 095645/Z/11/Z and EU FP7 EpiGeneSys and BLUEPRINT.

Author information

Author notes

    • Sébastien A Smallwood
    •  & Heather J Lee

    These authors contributed equally to this work.

    • Wolf Reik
    •  & Gavin Kelsey

    These authors jointly directed this work.

Affiliations

  1. Epigenetics Programme, Babraham Institute, Cambridge, UK.

    • Sébastien A Smallwood
    • , Heather J Lee
    • , Heba Saadeh
    • , Julian Peat
    • , Wolf Reik
    •  & Gavin Kelsey
  2. Wellcome Trust Sanger Institute, Cambridge, UK.

    • Heather J Lee
    •  & Wolf Reik
  3. European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK.

    • Christof Angermueller
    •  & Oliver Stegle
  4. Bioinformatics Group, Babraham Institute, Cambridge, UK.

    • Felix Krueger
    •  & Simon R Andrews
  5. Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.

    • Wolf Reik
    •  & Gavin Kelsey

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Contributions

S.A.S. and H.J.L. designed the study, prepared scBS-seq libraries, analyzed data and wrote the manuscript. F.K., H.S. and S.R.A. performed sequence mapping and analyzed data. J.P. contributed to technical developments. C.A. and O.S. analyzed data. O.S. provided advice on statistical analyses. W.R. and G.K. supervised the study and wrote the manuscript.

Competing interests

W.R. is a consultant to Cambridge Epigenetix Ltd.

Corresponding authors

Correspondence to Wolf Reik or Gavin Kelsey.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–13

Excel files

  1. 1.

    Supplementary Table 1

    Characteristics and statistics of scBS-seq libraries.

  2. 2.

    Supplementary Table 2

    Representation of regulatory regions in ESC scBS-seq datasets.

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DOI

https://doi.org/10.1038/nmeth.3035

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