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G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

Macaulay, Iain C. and Haerty, Wilfried and Kumar, Parveen and Li, Yang I. and Hu, Tim Xiaoming and Teng, Mabel J. and Goolam, Mubeen and Saurat, Nathalie and Coupland, Paul and Shirley, Lesley M. and Smith, Miriam and Van der Aa, Niels and Banerjee, Ruby and Ellis, Peter D. and Quail, Michael A and Swerdlow, Harold P. and Zernicka-Goetz, Magdalena and Livesey, Frederick J. and Ponting, Chris P. and Voet, Thierry (2015) G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nature Methods, 12 (6). pp. 519-522. ISSN 1548-7091. https://resolver.caltech.edu/CaltechAUTHORS:20190405-170315821

[img] Image (JPEG) (Supplementary Figure 1 : Performance of G&T-seq whole-genome amplification in HCC38 and HCC38-BL cells) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 2 : Performance of G&T-seq whole-transcriptome amplification in HCC38 and HCC38-BL cells) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 3 : Sequence coverage over transcript length and intronic and gene flanking regions in single-cell G&T-seq transcriptome data) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 4 : Comparison of RNA-seq data generated with the G&T-seq and conventional Smart-seq2 protocols) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 5 : Interphase FISH to detect trisomy 11 in a subset of HCC38-BL cells) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 6 : Relationship between chromosomal copy number and chromosome-wide expression in a mouse embryo at the eight-cell stage) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 7 : Relationship between chromosomal copy number and chromosome-wide expression in a mouse embryo at the eight-cell stage) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 8 : Relationship between chromosomal copy number and chromosome-wide expression in a mouse embryo at the eight-cell stage) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 9 : Relationship between chromosomal copy number and chromosome-wide expression in a mouse embryo at the eight-cell stage) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 10 : Relationship between chromosomal-arm copy number and chromosome-arm-wide expression in iPSC-derived neurons) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 11 : Detection of a coding interchromosomal fusion in the genome and transcriptome of a single cell) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 12 : Confirmation of MTAP-PCDH7 expression and detection of the associated genomic fusion by qPCR) - Supplemental Material
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[img] PDF (Supplementary Figures 1–12, and Supplementary Tables 1 and 2) - Supplemental Material
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[img] MS Excel (Supplementary Data 1. Excel spreadsheet containing sequencing and QC metrics for all cells presented in the paper) - Supplemental Material
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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/nmeth.3370DOIArticle
https://rdcu.be/bvGBCPublisherFree ReadCube access
ORCID:
AuthorORCID
Li, Yang I.0000-0002-0736-251X
Smith, Miriam0000-0002-3321-1432
Zernicka-Goetz, Magdalena0000-0002-7004-2471
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.
Funders:
Funding AgencyGrant Number
Wellcome TrustUNSPECIFIED
Fonds Wetenschappelijk Onderzoek (FWO)FWO-G.0687.12
Katholieke Universiteit LeuvenPFV/10/016
Fonds Wetenschappelijk Onderzoek (FWO)FWO-1.1.H28.12
Medical Research Council (UK)UNSPECIFIED
European Research Council (ERC)262055
St. John's College, CambridgeUNSPECIFIED
New Zealand Woolf-Fisher TrustUNSPECIFIED
University of OxfordUNSPECIFIED
Issue or Number:6
Record Number:CaltechAUTHORS:20190405-170315821
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190405-170315821
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:94544
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:09 Apr 2019 22:44
Last Modified:09 Mar 2020 13:19

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