Published June 2015
| Supplemental Material
Journal Article
Open
G&T-seq: parallel sequencing of single-cell genomes and transcriptomes
- Creators
- Macaulay, Iain C.
- Haerty, Wilfried
- Kumar, Parveen
-
Li, Yang I.
- Hu, Tim Xiaoming
- Teng, Mabel J.
- Goolam, Mubeen
- Saurat, Nathalie
- Coupland, Paul
- Shirley, Lesley M.
-
Smith, Miriam
- Van der Aa, Niels
- Banerjee, Ruby
- Ellis, Peter D.
- Quail, Michael A
- Swerdlow, Harold P.
-
Zernicka-Goetz, Magdalena
- Livesey, Frederick J.
- Ponting, Chris P.
- Voet, Thierry
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.
Additional Information
© 2015 Nature Publishing Group. Received 18 November 2014; accepted 27 March 2015; published online 27 April 2015. 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). Wilfried Haerty & Parveen Kumar - These authors contributed equally to this work. Chris P. Ponting & Thierry Voet - These authors jointly directed this work. Author 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. Code availability.: Custom code is available upon request. Accession codes. Human data are available from the European Genome-phenome Archive (EGA) with accession number EGAS00001001204. Mouse data are available from ArrayExpress with accession number E-ERAD-381. The authors declare no competing financial interests.Attached Files
Supplemental Material - nmeth.3370-S1.pdf
Supplemental Material - nmeth.3370-S2.xlsx
Supplemental Material - nmeth.3370-SF1.jpg
Supplemental Material - nmeth.3370-SF10.jpg
Supplemental Material - nmeth.3370-SF11.jpg
Supplemental Material - nmeth.3370-SF12.jpg
Supplemental Material - nmeth.3370-SF2.jpg
Supplemental Material - nmeth.3370-SF3.jpg
Supplemental Material - nmeth.3370-SF4.jpg
Supplemental Material - nmeth.3370-SF5.jpg
Supplemental Material - nmeth.3370-SF6.jpg
Supplemental Material - nmeth.3370-SF7.jpg
Supplemental Material - nmeth.3370-SF8.jpg
Supplemental Material - nmeth.3370-SF9.jpg
Files
nmeth.3370-SF4.jpg
Files
(18.8 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:e25879ec0ac521d6422ead7c036e908a
|
40.0 kB | Preview Download |
|
md5:4c2b12e12063f379a0ae53bf46596b44
|
32.7 kB | Preview Download |
|
md5:6edde81bd962e64c8c90760cfeb906e6
|
70.8 kB | Preview Download |
|
md5:9b4420f20fee81cfdf660e1b156450b2
|
29.1 kB | Preview Download |
|
md5:4b5f64a2cb60428e16403fe03baf8d20
|
38.3 kB | Preview Download |
|
md5:5b33a3c3b5d97f96c5e85957cf61f730
|
34.6 kB | Preview Download |
|
md5:40a69d395f1618b5775cc5f35fc68264
|
27.1 kB | Preview Download |
|
md5:336071261ae115e9d92c2072c5c0abaf
|
83.8 kB | Preview Download |
|
md5:4b32bc429cb4e17ca253fec7d0e30b12
|
18.2 MB | Preview Download |
|
md5:e01c6894148b6fc4c5c91469199d3b33
|
88.7 kB | Download |
|
md5:f72953afe3a2467d313f6583cb1797a8
|
70.5 kB | Preview Download |
|
md5:5ec25d49f852ddb3615b6e05fe9cbc59
|
23.3 kB | Preview Download |
|
md5:0e31a49cf266d79473ea2d9857634e14
|
31.7 kB | Preview Download |
|
md5:e3a770f4bd434cbcbce89f401e57a329
|
31.2 kB | Preview Download |
Additional details
- Eprint ID
- 94544
- DOI
- 10.1038/nmeth.3370
- Resolver ID
- CaltechAUTHORS:20190405-170315821
- Wellcome Trust
- FWO-G.0687.12
- Fonds Wetenschappelijk Onderzoek (FWO)
- PFV/10/016
- Katholieke Universiteit Leuven
- FWO-1.1.H28.12
- Fonds Wetenschappelijk Onderzoek (FWO)
- Medical Research Council (UK)
- 262055
- European Research Council (ERC)
- St. John's College, Cambridge
- New Zealand Woolf-Fisher Trust
- University of Oxford
- Created
-
2019-04-09Created from EPrint's datestamp field
- Updated
-
2021-11-16Created from EPrint's last_modified field