Literature DB >> 25915121

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

Iain C Macaulay1, Wilfried Haerty2, Parveen Kumar3, Yang I Li2, Tim Xiaoming Hu2, Mabel J Teng4, Mubeen Goolam5, Nathalie Saurat6, Paul Coupland7, Lesley M Shirley7, Miriam Smith7, Niels Van der Aa3, Ruby Banerjee8, Peter D Ellis7, Michael A Quail7, Harold P Swerdlow7, Magdalena Zernicka-Goetz5, Frederick J Livesey6, Chris P Ponting9, Thierry Voet10.   

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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Year:  2015        PMID: 25915121     DOI: 10.1038/nmeth.3370

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  45 in total

1.  BLAT--the BLAST-like alignment tool.

Authors:  W James Kent
Journal:  Genome Res       Date:  2002-04       Impact factor: 9.043

2.  CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.

Authors:  Tamar Hashimshony; Florian Wagner; Noa Sher; Itai Yanai
Journal:  Cell Rep       Date:  2012-08-30       Impact factor: 9.423

3.  Combined transcriptome and genome analysis of single micrometastatic cells.

Authors:  Christoph A Klein; Stefan Seidl; Karina Petat-Dutter; Sonja Offner; Jochen B Geigl; Oleg Schmidt-Kittler; Nicole Wendler; Bernward Passlick; Rudolf M Huber; Günter Schlimok; Patrick A Baeuerle; Gert Riethmüller
Journal:  Nat Biotechnol       Date:  2002-04       Impact factor: 54.908

Review 4.  The impact of translocations and gene fusions on cancer causation.

Authors:  Felix Mitelman; Bertil Johansson; Fredrik Mertens
Journal:  Nat Rev Cancer       Date:  2007-03-15       Impact factor: 60.716

Review 5.  The cancer genome.

Authors:  Michael R Stratton; Peter J Campbell; P Andrew Futreal
Journal:  Nature       Date:  2009-04-09       Impact factor: 49.962

6.  Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.

Authors:  Diego Adhemar Jaitin; Ephraim Kenigsberg; Hadas Keren-Shaul; Naama Elefant; Franziska Paul; Irina Zaretsky; Alexander Mildner; Nadav Cohen; Steffen Jung; Amos Tanay; Ido Amit
Journal:  Science       Date:  2014-02-14       Impact factor: 47.728

7.  Bayesian approach to single-cell differential expression analysis.

Authors:  Peter V Kharchenko; Lev Silberstein; David T Scadden
Journal:  Nat Methods       Date:  2014-05-18       Impact factor: 28.547

8.  Integrated genome and transcriptome sequencing of the same cell.

Authors:  Siddharth S Dey; Lennart Kester; Bastiaan Spanjaard; Magda Bienko; Alexander van Oudenaarden
Journal:  Nat Biotechnol       Date:  2015-01-19       Impact factor: 54.908

9.  Next-generation sequencing of disseminated tumor cells.

Authors:  Elen K Møller; Parveen Kumar; Thierry Voet; April Peterson; Peter Van Loo; Randi R Mathiesen; Renathe Fjelldal; Jason Grundstad; Elin Borgen; Lars O Baumbusch; Bjørn Naume; Anne-Lise Børresen-Dale; Kevin P White; Silje Nord; Vessela N Kristensen
Journal:  Front Oncol       Date:  2013-12-31       Impact factor: 6.244

10.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.

Authors:  Daehwan Kim; Geo Pertea; Cole Trapnell; Harold Pimentel; Ryan Kelley; Steven L Salzberg
Journal:  Genome Biol       Date:  2013-04-25       Impact factor: 13.583

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  250 in total

Review 1.  Single-cell epigenomics: techniques and emerging applications.

Authors:  Omer Schwartzman; Amos Tanay
Journal:  Nat Rev Genet       Date:  2015-10-13       Impact factor: 53.242

Review 2.  The niche in single-cell technologies.

Authors:  Giacomo Donati
Journal:  Immunol Cell Biol       Date:  2015-12-22       Impact factor: 5.126

Review 3.  Single-cell genome sequencing: current state of the science.

Authors:  Charles Gawad; Winston Koh; Stephen R Quake
Journal:  Nat Rev Genet       Date:  2016-01-25       Impact factor: 53.242

4.  Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells.

Authors:  Arnav Moudgil; Michael N Wilkinson; Xuhua Chen; June He; Alexander J Cammack; Michael J Vasek; Tomás Lagunas; Zongtai Qi; Matthew A Lalli; Chuner Guo; Samantha A Morris; Joseph D Dougherty; Robi D Mitra
Journal:  Cell       Date:  2020-07-24       Impact factor: 41.582

Review 5.  Beyond genome-wide significance: integrative approaches to the interpretation and extension of GWAS findings for alcohol use disorder.

Authors:  Jessica E Salvatore; Shizhong Han; Sean P Farris; Kristin M Mignogna; Michael F Miles; Arpana Agrawal
Journal:  Addict Biol       Date:  2018-01-09       Impact factor: 4.280

6.  Single Cell Genomics for Tumor Heterogeneity.

Authors:  Hae-Ock Lee; Woong-Yang Park
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

7.  High-throughput full-length single-cell mRNA-seq of rare cells.

Authors:  Chin Chun Ooi; Gary L Mantalas; Winston Koh; Norma F Neff; Teruaki Fuchigami; Dawson J Wong; Robert J Wilson; Seung-Min Park; Sanjiv S Gambhir; Stephen R Quake; Shan X Wang
Journal:  PLoS One       Date:  2017-11-29       Impact factor: 3.240

Review 8.  Mapping chromatin modifications at the single cell level.

Authors:  Connor H Ludwig; Lacramioara Bintu
Journal:  Development       Date:  2019-06-27       Impact factor: 6.868

Review 9.  Advancing Cancer Research and Medicine with Single-Cell Genomics.

Authors:  Bora Lim; Yiyun Lin; Nicholas Navin
Journal:  Cancer Cell       Date:  2020-04-13       Impact factor: 31.743

Review 10.  Tumour heterogeneity and metastasis at single-cell resolution.

Authors:  Devon A Lawson; Kai Kessenbrock; Ryan T Davis; Nicholas Pervolarakis; Zena Werb
Journal:  Nat Cell Biol       Date:  2018-11-26       Impact factor: 28.824

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