Literature DB >> 19015660

RNA-Seq: a revolutionary tool for transcriptomics.

Zhong Wang1, Mark Gerstein, Michael Snyder.   

Abstract

RNA-Seq is a recently developed approach to transcriptome profiling that uses deep-sequencing technologies. Studies using this method have already altered our view of the extent and complexity of eukaryotic transcriptomes. RNA-Seq also provides a far more precise measurement of levels of transcripts and their isoforms than other methods. This article describes the RNA-Seq approach, the challenges associated with its application, and the advances made so far in characterizing several eukaryote transcriptomes.

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Year:  2009        PMID: 19015660      PMCID: PMC2949280          DOI: 10.1038/nrg2484

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  43 in total

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Journal:  Nat Biotechnol       Date:  2000-06       Impact factor: 54.908

2.  High-throughput methods for the large-scale analysis of gene function by transposon tagging.

Authors:  A Kumar; S A des Etages; P S Coelho; G S Roeder; M Snyder
Journal:  Methods Enzymol       Date:  2000       Impact factor: 1.600

3.  The RNA binding protein Pub1 modulates the stability of transcripts containing upstream open reading frames.

Authors:  M J Ruiz-Echevarría; S W Peltz
Journal:  Cell       Date:  2000-06-23       Impact factor: 41.582

4.  Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays.

Authors:  Tyson A Clark; Charles W Sugnet; Manuel Ares
Journal:  Science       Date:  2002-05-03       Impact factor: 47.728

5.  Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.

Authors:  Toshiyuki Shiraki; Shinji Kondo; Shintaro Katayama; Kazunori Waki; Takeya Kasukawa; Hideya Kawaji; Rimantas Kodzius; Akira Watahiki; Mari Nakamura; Takahiro Arakawa; Shiro Fukuda; Daisuke Sasaki; Anna Podhajska; Matthias Harbers; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki
Journal:  Proc Natl Acad Sci U S A       Date:  2003-12-08       Impact factor: 11.205

6.  Empirical analysis of transcriptional activity in the Arabidopsis genome.

Authors:  Kayoko Yamada; Jun Lim; Joseph M Dale; Huaming Chen; Paul Shinn; Curtis J Palm; Audrey M Southwick; Hank C Wu; Christopher Kim; Michelle Nguyen; Paul Pham; Rosa Cheuk; George Karlin-Newmann; Shirley X Liu; Bao Lam; Hitomi Sakano; Troy Wu; Guixia Yu; Molly Miranda; Hong L Quach; Matthew Tripp; Charlie H Chang; Jeong M Lee; Mitsue Toriumi; Marie M H Chan; Carolyn C Tang; Courtney S Onodera; Justine M Deng; Kenji Akiyama; Yasser Ansari; Takahiro Arakawa; Jenny Banh; Fumika Banno; Leah Bowser; Shelise Brooks; Piero Carninci; Qimin Chao; Nathan Choy; Akiko Enju; Andrew D Goldsmith; Mani Gurjal; Nancy F Hansen; Yoshihide Hayashizaki; Chanda Johnson-Hopson; Vickie W Hsuan; Kei Iida; Meagan Karnes; Shehnaz Khan; Eric Koesema; Junko Ishida; Paul X Jiang; Ted Jones; Jun Kawai; Asako Kamiya; Cristina Meyers; Maiko Nakajima; Mari Narusaka; Motoaki Seki; Tetsuya Sakurai; Masakazu Satou; Racquel Tamse; Maria Vaysberg; Erika K Wallender; Cecilia Wong; Yuki Yamamura; Shiaulou Yuan; Kazuo Shinozaki; Ronald W Davis; Athanasios Theologis; Joseph R Ecker
Journal:  Science       Date:  2003-10-31       Impact factor: 47.728

Review 7.  Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms.

Authors:  Jeanette Reinartz; Eddy Bruyns; Jing-Zhong Lin; Tim Burcham; Sydney Brenner; Ben Bowen; Michael Kramer; Rick Woychik
Journal:  Brief Funct Genomic Proteomic       Date:  2002-02

8.  Large-scale analysis of the yeast genome by transposon tagging and gene disruption.

Authors:  P Ross-Macdonald; P S Coelho; T Roemer; S Agarwal; A Kumar; R Jansen; K H Cheung; A Sheehan; D Symoniatis; L Umansky; M Heidtman; F K Nelson; H Iwasaki; K Hager; M Gerstein; P Miller; G S Roeder; M Snyder
Journal:  Nature       Date:  1999-11-25       Impact factor: 49.962

9.  Gene discovery in dbEST.

Authors:  M S Boguski; C M Tolstoshev; D E Bassett
Journal:  Science       Date:  1994-09-30       Impact factor: 47.728

10.  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

Authors:  Daniela S Gerhard; Lukas Wagner; Elise A Feingold; Carolyn M Shenmen; Lynette H Grouse; Greg Schuler; Steven L Klein; Susan Old; Rebekah Rasooly; Peter Good; Mark Guyer; Allison M Peck; Jeffery G Derge; David Lipman; Francis S Collins; Wonhee Jang; Steven Sherry; Mike Feolo; Leonie Misquitta; Eduardo Lee; Kirill Rotmistrovsky; Susan F Greenhut; Carl F Schaefer; Kenneth Buetow; Tom I Bonner; David Haussler; Jim Kent; Mark Kiekhaus; Terry Furey; Michael Brent; Christa Prange; Kirsten Schreiber; Nicole Shapiro; Narayan K Bhat; Ralph F Hopkins; Florence Hsie; Tom Driscoll; M Bento Soares; Tom L Casavant; Todd E Scheetz; Michael J Brown-stein; Ted B Usdin; Shiraki Toshiyuki; Piero Carninci; Yulan Piao; Dawood B Dudekula; Minoru S H Ko; Koichi Kawakami; Yutaka Suzuki; Sumio Sugano; C E Gruber; M R Smith; Blake Simmons; Troy Moore; Richard Waterman; Stephen L Johnson; Yijun Ruan; Chia Lin Wei; S Mathavan; Preethi H Gunaratne; Jiaqian Wu; Angela M Garcia; Stephen W Hulyk; Edwin Fuh; Ye Yuan; Anna Sneed; Carla Kowis; Anne Hodgson; Donna M Muzny; John McPherson; Richard A Gibbs; Jessica Fahey; Erin Helton; Mark Ketteman; Anuradha Madan; Stephanie Rodrigues; Amy Sanchez; Michelle Whiting; Anup Madari; Alice C Young; Keith D Wetherby; Steven J Granite; Peggy N Kwong; Charles P Brinkley; Russell L Pearson; Gerard G Bouffard; Robert W Blakesly; Eric D Green; Mark C Dickson; Alex C Rodriguez; Jane Grimwood; Jeremy Schmutz; Richard M Myers; Yaron S N Butterfield; Malachi Griffith; Obi L Griffith; Martin I Krzywinski; Nancy Liao; Ryan Morin; Ryan Morrin; Diana Palmquist; Anca S Petrescu; Ursula Skalska; Duane E Smailus; Jeff M Stott; Angelique Schnerch; Jacqueline E Schein; Steven J M Jones; Robert A Holt; Agnes Baross; Marco A Marra; Sandra Clifton; Kathryn A Makowski; Stephanie Bosak; Joel Malek
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

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  2000 in total

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Journal:  Dev Biol       Date:  2012-06-01       Impact factor: 3.582

2.  mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain.

Authors:  Paul Hammer; Michaela S Banck; Ronny Amberg; Cheng Wang; Gabriele Petznick; Shujun Luo; Irina Khrebtukova; Gary P Schroth; Peter Beyerlein; Andreas S Beutler
Journal:  Genome Res       Date:  2010-05-07       Impact factor: 9.043

3.  A shortcut for multiple testing on the directed acyclic graph of gene ontology.

Authors:  Garrett Saunders; John R Stevens; S Clay Isom
Journal:  BMC Bioinformatics       Date:  2014-11-01       Impact factor: 3.169

4.  Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.

Authors:  Jennifer M Hurley; Arko Dasgupta; Jillian M Emerson; Xiaoying Zhou; Carol S Ringelberg; Nicole Knabe; Anna M Lipzen; Erika A Lindquist; Christopher G Daum; Kerrie W Barry; Igor V Grigoriev; Kristina M Smith; James E Galagan; Deborah Bell-Pedersen; Michael Freitag; Chao Cheng; Jennifer J Loros; Jay C Dunlap
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-31       Impact factor: 11.205

Review 5.  Advancing insights into stem cell niche complexities with next-generation technologies.

Authors:  Nicholas Heitman; Nivedita Saxena; Michael Rendl
Journal:  Curr Opin Cell Biol       Date:  2018-07-19       Impact factor: 8.382

6.  Single sample sequencing (S3EQ) of epigenome and transcriptome in nucleus accumbens.

Authors:  S J Xu; E A Heller
Journal:  J Neurosci Methods       Date:  2018-07-18       Impact factor: 2.390

Review 7.  Targeted therapy in gastric cancer: personalizing cancer treatment based on patient genome.

Authors:  Sun Min Lim; Jae Yun Lim; Jae Yong Cho
Journal:  World J Gastroenterol       Date:  2014-02-28       Impact factor: 5.742

8.  Downregulation of the acetyl-CoA metabolic network in adipose tissue of obese diabetic individuals and recovery after weight loss.

Authors:  Harish Dharuri; Peter A C 't Hoen; Jan B van Klinken; Peter Henneman; Jeroen F J Laros; Mirjam A Lips; Fatiha El Bouazzaoui; Gert-Jan B van Ommen; Ignace Janssen; Bert van Ramshorst; Bert A van Wagensveld; Hanno Pijl; Ko Willems van Dijk; Vanessa van Harmelen
Journal:  Diabetologia       Date:  2014-08-07       Impact factor: 10.122

9.  Novel identification of STAT1 as a crucial mediator of ETV6-NTRK3-induced tumorigenesis.

Authors:  Jinah Park; Junil Kim; Bora Park; Kyung-Min Yang; Eun Jin Sun; Cristina E Tognon; Poul H Sorensen; Seong-Jin Kim
Journal:  Oncogene       Date:  2018-02-02       Impact factor: 9.867

10.  RNentropy: an entropy-based tool for the detection of significant variation of gene expression across multiple RNA-Seq experiments.

Authors:  Federico Zambelli; Francesca Mastropasqua; Ernesto Picardi; Anna Maria D'Erchia; Graziano Pesole; Giulio Pavesi
Journal:  Nucleic Acids Res       Date:  2018-05-04       Impact factor: 16.971

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