Literature DB >> 19668204

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis.

Christopher D Armour1, John C Castle, Ronghua Chen, Tomas Babak, Patrick Loerch, Stuart Jackson, Jyoti K Shah, John Dey, Carol A Rohl, Jason M Johnson, Christopher K Raymond.   

Abstract

We developed a procedure for the preparation of whole transcriptome cDNA libraries depleted of ribosomal RNA from only 1 microg of total RNA. The method relies on a collection of short, computationally selected oligonucleotides, called 'not-so-random' (NSR) primers, to obtain full-length, strand-specific representation of nonribosomal RNA transcripts. In this study we validated the technique by profiling human whole brain and universal human reference RNA using ultra-high-throughput sequencing.

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Year:  2009        PMID： 19668204     DOI： 10.1038/nmeth.1360

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


  15 in total

1.  Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs.

Authors:  Christopher K Raymond; Brian S Roberts; Phillip Garrett-Engele; Lee P Lim; Jason M Johnson
Journal:  RNA       Date:  2005-11       Impact factor: 4.942

2.  The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.

Authors:  Leming Shi; Laura H Reid; Wendell D Jones; Richard Shippy; Janet A Warrington; Shawn C Baker; Patrick J Collins; Francoise de Longueville; Ernest S Kawasaki; Kathleen Y Lee; Yuling Luo; Yongming Andrew Sun; James C Willey; Robert A Setterquist; Gavin M Fischer; Weida Tong; Yvonne P Dragan; David J Dix; Felix W Frueh; Frederico M Goodsaid; Damir Herman; Roderick V Jensen; Charles D Johnson; Edward K Lobenhofer; Raj K Puri; Uwe Schrf; Jean Thierry-Mieg; Charles Wang; Mike Wilson; Paul K Wolber; Lu Zhang; Shashi Amur; Wenjun Bao; Catalin C Barbacioru; Anne Bergstrom Lucas; Vincent Bertholet; Cecilie Boysen; Bud Bromley; Donna Brown; Alan Brunner; Roger Canales; Xiaoxi Megan Cao; Thomas A Cebula; James J Chen; Jing Cheng; Tzu-Ming Chu; Eugene Chudin; John Corson; J Christopher Corton; Lisa J Croner; Christopher Davies; Timothy S Davison; Glenda Delenstarr; Xutao Deng; David Dorris; Aron C Eklund; Xiao-hui Fan; Hong Fang; Stephanie Fulmer-Smentek; James C Fuscoe; Kathryn Gallagher; Weigong Ge; Lei Guo; Xu Guo; Janet Hager; Paul K Haje; Jing Han; Tao Han; Heather C Harbottle; Stephen C Harris; Eli Hatchwell; Craig A Hauser; Susan Hester; Huixiao Hong; Patrick Hurban; Scott A Jackson; Hanlee Ji; Charles R Knight; Winston P Kuo; J Eugene LeClerc; Shawn Levy; Quan-Zhen Li; Chunmei Liu; Ying Liu; Michael J Lombardi; Yunqing Ma; Scott R Magnuson; Botoul Maqsodi; Tim McDaniel; Nan Mei; Ola Myklebost; Baitang Ning; Natalia Novoradovskaya; Michael S Orr; Terry W Osborn; Adam Papallo; Tucker A Patterson; Roger G Perkins; Elizabeth H Peters; Ron Peterson; Kenneth L Philips; P Scott Pine; Lajos Pusztai; Feng Qian; Hongzu Ren; Mitch Rosen; Barry A Rosenzweig; Raymond R Samaha; Mark Schena; Gary P Schroth; Svetlana Shchegrova; Dave D Smith; Frank Staedtler; Zhenqiang Su; Hongmei Sun; Zoltan Szallasi; Zivana Tezak; Danielle Thierry-Mieg; Karol L Thompson; Irina Tikhonova; Yaron Turpaz; Beena Vallanat; Christophe Van; Stephen J Walker; Sue Jane Wang; Yonghong Wang; Russ Wolfinger; Alex Wong; Jie Wu; Chunlin Xiao; Qian Xie; Jun Xu; Wen Yang; Liang Zhang; Sheng Zhong; Yaping Zong; William Slikker
Journal:  Nat Biotechnol       Date:  2006-09       Impact factor: 54.908

3.  Counterselection of prokaryotic ribosomal RNA during reverse transcription using non-random hexameric oligonucleotides.

Authors:  J M Gonzalez; F T Robb
Journal:  J Microbiol Methods       Date:  2007-09-26       Impact factor: 2.363

4.  Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.

Authors:  Ryan Morin; Matthew Bainbridge; Anthony Fejes; Martin Hirst; Martin Krzywinski; Trevor Pugh; Helen McDonald; Richard Varhol; Steven Jones; Marco Marra
Journal:  Biotechniques       Date:  2008-07       Impact factor: 1.993

5.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

6.  Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Authors:  Nicole Cloonan; Alistair R R Forrest; Gabriel Kolle; Brooke B A Gardiner; Geoffrey J Faulkner; Mellissa K Brown; Darrin F Taylor; Anita L Steptoe; Shivangi Wani; Graeme Bethel; Alan J Robertson; Andrew C Perkins; Stephen J Bruce; Clarence C Lee; Swati S Ranade; Heather E Peckham; Jonathan M Manning; Kevin J McKernan; Sean M Grimmond
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

7.  The eukaryotic genome as an RNA machine.

Authors:  Paulo P Amaral; Marcel E Dinger; Tim R Mercer; John S Mattick
Journal:  Science       Date:  2008-03-28       Impact factor: 47.728

8.  Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing.

Authors:  D R Yoder-Himes; P S G Chain; Y Zhu; O Wurtzel; E M Rubin; James M Tiedje; R Sorek
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-20       Impact factor: 11.205

9.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.

Authors:  Mitchell Guttman; Ido Amit; Manuel Garber; Courtney French; Michael F Lin; David Feldser; Maite Huarte; Or Zuk; Bryce W Carey; John P Cassady; Moran N Cabili; Rudolf Jaenisch; Tarjei S Mikkelsen; Tyler Jacks; Nir Hacohen; Bradley E Bernstein; Manolis Kellis; Aviv Regev; John L Rinn; Eric S Lander
Journal:  Nature       Date:  2009-02-01       Impact factor: 49.962

10.  Global survey of genomic imprinting by transcriptome sequencing.

Authors:  Tomas Babak; Brian Deveale; Christopher Armour; Christopher Raymond; Michele A Cleary; Derek van der Kooy; Jason M Johnson; Lee P Lim
Journal:  Curr Biol       Date:  2008-11-25       Impact factor: 10.834
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  93 in total

1.  A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation.

Authors:  Kristi Fox-Walsh; Jeremy Davis-Turak; Yu Zhou; Hairi Li; Xiang-Dong Fu
Journal:  Genomics       Date:  2011-04-15       Impact factor: 5.736

Review 2.  Microbe hunting.

Authors:  W Ian Lipkin
Journal:  Microbiol Mol Biol Rev       Date:  2010-09       Impact factor: 11.056

3.  A spatial and temporal map of C. elegans gene expression.

Authors:  W Clay Spencer; Georg Zeller; Joseph D Watson; Stefan R Henz; Kathie L Watkins; Rebecca D McWhirter; Sarah Petersen; Vipin T Sreedharan; Christian Widmer; Jeanyoung Jo; Valerie Reinke; Lisa Petrella; Susan Strome; Stephen E Von Stetina; Menachem Katz; Shai Shaham; Gunnar Rätsch; David M Miller
Journal:  Genome Res       Date:  2010-12-22       Impact factor: 9.043

Review 4.  RNA sequencing: advances, challenges and opportunities.

Authors:  Fatih Ozsolak; Patrice M Milos
Journal:  Nat Rev Genet       Date:  2010-12-30       Impact factor: 53.242

Review 5.  Single-molecule direct RNA sequencing without cDNA synthesis.

Authors:  Fatih Ozsolak; Patrice M Milos
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-03-14       Impact factor: 9.957

Review 6.  Dual RNA-seq of pathogen and host.

Authors:  Alexander J Westermann; Stanislaw A Gorski; Jörg Vogel
Journal:  Nat Rev Microbiol       Date:  2012-09       Impact factor: 60.633

7.  Gene expression variations in microsatellite stable and unstable colon cancer cells.

Authors:  Marjun P Duldulao; Wendy Lee; Maithao Le; Zhenbin Chen; Wenyan Li; Jinhui Wang; Harry Gao; Haiquing Li; Joseph Kim; Julio Garcia-Aguilar
Journal:  J Surg Res       Date:  2011-07-07       Impact factor: 2.192

Review 8.  Computation for ChIP-seq and RNA-seq studies.

Authors:  Shirley Pepke; Barbara Wold; Ali Mortazavi
Journal:  Nat Methods       Date:  2009-11       Impact factor: 28.547

Review 9.  RNA-Seq methods for transcriptome analysis.

Authors:  Radmila Hrdlickova; Masoud Toloue; Bin Tian
Journal:  Wiley Interdiscip Rev RNA       Date:  2016-05-19       Impact factor: 9.957

10.  Global analysis of the Burkholderia thailandensis quorum sensing-controlled regulon.

Authors:  Charlotte Majerczyk; Mitchell Brittnacher; Michael Jacobs; Christopher D Armour; Mathew Radey; Emily Schneider; Somsak Phattarasokul; Richard Bunt; E Peter Greenberg
Journal:  J Bacteriol       Date:  2014-01-24       Impact factor: 3.490
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