RNA-Seq: a revolutionary tool for transcriptomics

被引:8789
作者
Wang, Zhong [1 ]
Gerstein, Mark [2 ]
Snyder, Michael [1 ]
机构
[1] Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA
[2] Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA
关键词
LARGE-SCALE ANALYSIS; GENE-EXPRESSION; YEAST GENOME; CAP ANALYSIS; DISCOVERY; IDENTIFICATION; MAPS;
D O I
10.1038/nrg2484
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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.
引用
收藏
页码:57 / 63
页数:7
相关论文
共 43 条
[1]   SNP discovery via 454 transcriptome sequencing [J].
Barbazuk, W. Brad ;
Emrich, Scott J. ;
Chen, Hsin D. ;
Li, Li ;
Schnable, Patrick S. .
PLANT JOURNAL, 2007, 51 (05) :910-918
[2]   How does RNA editing affect dsRNA-mediated gene silencing? [J].
Bass, B. L. .
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY, 2006, 71 :285-292
[3]   Global identification of human transcribed sequences with genome tiling arrays [J].
Bertone, P ;
Stolc, V ;
Royce, TE ;
Rozowsky, JS ;
Urban, AE ;
Zhu, XW ;
Rinn, JL ;
Tongprasit, W ;
Samanta, M ;
Weissman, S ;
Gerstein, M ;
Snyder, M .
SCIENCE, 2004, 306 (5705) :2242-2246
[4]   GENE DISCOVERY IN DBEST [J].
BOGUSKI, MS ;
TOLSTOSHEV, CM ;
BASSETT, DE .
SCIENCE, 1994, 265 (5181) :1993-1994
[5]   Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays [J].
Brenner, S ;
Johnson, M ;
Bridgham, J ;
Golda, G ;
Lloyd, DH ;
Johnson, D ;
Luo, SJ ;
McCurdy, S ;
Foy, M ;
Ewan, M ;
Roth, R ;
George, D ;
Eletr, S ;
Albrecht, G ;
Vermaas, E ;
Williams, SR ;
Moon, K ;
Burcham, T ;
Pallas, M ;
DuBridge, RB ;
Kirchner, J ;
Fearon, K ;
Mao, J ;
Corcoran, K .
NATURE BIOTECHNOLOGY, 2000, 18 (06) :630-634
[6]   Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing [J].
Campbell, Peter J. ;
Stephens, Philip J. ;
Pleasance, Erin D. ;
O'Meara, Sarah ;
Li, Heng ;
Santarius, Thomas ;
Stebbings, Lucy A. ;
Leroy, Catherine ;
Edkins, Sarah ;
Hardy, Claire ;
Teague, Jon W. ;
Menzies, Andrew ;
Goodhead, Ian ;
Turner, Daniel J. ;
Clee, Christopher M. ;
Quail, Michael A. ;
Cox, Antony ;
Brown, Clive ;
Durbin, Richard ;
Hurles, Matthew E. ;
Edwards, Paul A. W. ;
Bignell, Graham R. ;
Stratton, Michael R. ;
Futreal, P. Andrew .
NATURE GENETICS, 2008, 40 (06) :722-729
[7]   Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution [J].
Cheng, J ;
Kapranov, P ;
Drenkow, J ;
Dike, S ;
Brubaker, S ;
Patel, S ;
Long, J ;
Stern, D ;
Tammana, H ;
Helt, G ;
Sementchenko, V ;
Piccolboni, A ;
Bekiranov, S ;
Bailey, DK ;
Ganesh, M ;
Ghosh, S ;
Bell, I ;
Gerhard, DS ;
Gingeras, TR .
SCIENCE, 2005, 308 (5725) :1149-1154
[8]   Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays [J].
Clark, TA ;
Sugnet, CW ;
Ares, M .
SCIENCE, 2002, 296 (5569) :907-910
[9]   Stem cell transcriptome profiling via massive-scale mRNA sequencing [J].
Cloonan, Nicole ;
Forrest, Alistair R. R. ;
Kolle, Gabriel ;
Gardiner, Brooke B. A. ;
Faulkner, Geoffrey J. ;
Brown, Mellissa K. ;
Taylor, Darrin F. ;
Steptoe, Anita L. ;
Wani, Shivangi ;
Bethel, Graeme ;
Robertson, Alan J. ;
Perkins, Andrew C. ;
Bruce, Stephen J. ;
Lee, Clarence C. ;
Ranade, Swati S. ;
Peckham, Heather E. ;
Manning, Jonathan M. ;
McKernan, Kevin J. ;
Grimmond, Sean M. .
NATURE METHODS, 2008, 5 (07) :613-619
[10]   A high-resolution map of transcription in the yeast genome [J].
David, L ;
Huber, W ;
Granovskaia, M ;
Toedling, J ;
Palm, CJ ;
Bofkin, L ;
Jones, T ;
Davis, RW ;
Steinmetz, LM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (14) :5320-5325