Abstract

The simultaneous sequencing of a single cell's genome and transcriptome offers a powerful means to dissect genetic variation and its effect on gene expression. Here we describe G&T-seq, a method for separating and sequencing genomic DNA and full-length mRNA from single cells. By applying G&T-seq to over 220 single cells from mice and humans, we discovered cellular properties that could not be inferred from DNA or RNA sequencing alone.

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Acknowledgements

We thank the Wellcome Trust Sanger Institute (UK) sequencing pipelines and F. Yang of the Cytogenetics Core Facility. This work was supported by the UK Wellcome Trust (to T.V. and C.P.P.) and funding from the Belgian Research Foundation Flanders (FWO) and the University of Leuven (KU Leuven, Belgium) to T.V. (FWO–G.0687.12; KU Leuven SymBioSys, PFV/10/016). N.V.d.A. is supported by an FWO scholarship (FWO–1.1.H28.12). W.H. and C.P.P. are funded by the UK Medical Research Council. L.M.S. was funded by the EU Seventh Framework Programme (FP7/2007-2013) under grant 262055. M.Z.-G. and the work in the lab are funded by the UK Wellcome Trust. M.G. is supported by a UK Mary Gray Studentship from St. John's College, Cambridge, UK. N.S. was supported by the New Zealand Woolf-Fisher Trust. F.J.L. is supported by a UK Wellcome Trust Senior Investigator award. M.J.T. is supported by a Wellcome Trust Sanger Institute Clinical Ph.D. Fellowship (UK). Y.I.L. was supported by a University of Oxford Nuffield Department of Medicine Prize Studentship, UK. Trisomy 21 iPSCs were obtained from the Harvard Stem Cell Institute (Cambridge, Massachusetts, USA), and control iPSCs were a gift from Y. Takashima (Cambridge Stem Cell Institute, Cambridge, UK).

Author information

Author notes

    • Yang I Li
    •  & Harold P Swerdlow

    Present addresses: Department of Genetics, Stanford University, Stanford, California, USA (Y.I.L.). New York Genome Center, New York, New York, USA (H.P.S.).

    • Wilfried Haerty
    •  & Parveen Kumar

    These authors contributed equally to this work.

    • Chris P Ponting
    •  & Thierry Voet

    These authors jointly directed this work.

Affiliations

  1. Sanger Institute–EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, UK.

    • Iain C Macaulay
    • , Chris P Ponting
    •  & Thierry Voet
  2. MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.

    • Wilfried Haerty
    • , Yang I Li
    • , Tim Xiaoming Hu
    •  & Chris P Ponting
  3. Department of Human Genetics, University of Leuven, Leuven, Belgium.

    • Parveen Kumar
    • , Niels Van der Aa
    •  & Thierry Voet
  4. Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Mabel J Teng
  5. Department of Physiology, Development and Neuroscience, Downing Site, University of Cambridge, Cambridge, UK.

    • Mubeen Goolam
    •  & Magdalena Zernicka-Goetz
  6. Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.

    • Nathalie Saurat
    •  & Frederick J Livesey
  7. Sequencing R&D, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Paul Coupland
    • , Lesley M Shirley
    • , Miriam Smith
    • , Peter D Ellis
    • , Michael A Quail
    •  & Harold P Swerdlow
  8. Cytogenetics Core Facility, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

    • Ruby Banerjee

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Contributions

I.C.M. developed the method, performed experiments, analyzed data and wrote the paper. W.H., P.K., Y.I.L. and T.X.H. analyzed data and prepared figures and text for the paper. M.J.T. performed experiments and assisted with method development. N.V.d.A. provided cells and assisted with method development. M.G. and M.Z.-G. provided mouse blastomeres. N.S. and F.J.L. provided iPSC-derived neurons. P.C., L.M.S., M.S., P.D.E., M.A.Q. and H.P.S. assisted with library preparation for targeted, HiSeq X and PacBio sequencing. R.B. performed cytogenetic analysis of cell lines. C.P.P. and T.V. acquired funding, oversaw the research, designed the method, analyzed data and wrote the paper. All authors read and approved the manuscript for submission.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Iain C Macaulay or Chris P Ponting or Thierry Voet.

Integrated supplementary information

Supplementary information

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    Supplementary Text and Figures

    Supplementary Figures 1–12, and Supplementary Tables 1 and 2

Excel files

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    Supplementary Data 1

    Excel spreadsheet containing sequencing and QC metrics for all cells presented in the paper.

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DOI

https://doi.org/10.1038/nmeth.3370

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