Literature DB >> 25730492

Simultaneous generation of many RNA-seq libraries in a single reaction.

Alexander A Shishkin1, Georgia Giannoukos2, Alper Kucukural3, Dawn Ciulla2, Michele Busby2, Christine Surka1, Jenny Chen4, Roby P Bhattacharyya2, Robert F Rudy2, Milesh M Patel2, Nathaniel Novod2, Deborah T Hung2, Andreas Gnirke2, Manuel Garber5, Mitchell Guttman1, Jonathan Livny2.   

Abstract

Although RNA-seq is a powerful tool, the considerable time and cost associated with library construction has limited its utilization for various applications. RNAtag-Seq, an approach to generate multiple RNA-seq libraries in a single reaction, lowers time and cost per sample, and it produces data on prokaryotic and eukaryotic samples that are comparable to those generated by traditional strand-specific RNA-seq approaches.

Entities:  

Mesh：

Year:  2015        PMID： 25730492      PMCID： PMC4712044          DOI： 10.1038/nmeth.3313

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


  34 in total

1.  Counting absolute numbers of molecules using unique molecular identifiers.

Authors:  Teemu Kivioja; Anna Vähärautio; Kasper Karlsson; Martin Bonke; Martin Enge; Sten Linnarsson; Jussi Taipale
Journal:  Nat Methods       Date:  2011-11-20       Impact factor: 28.547

Review 2.  Computational methods for transcriptome annotation and quantification using RNA-seq.

Authors:  Manuel Garber; Manfred G Grabherr; Mitchell Guttman; Cole Trapnell
Journal:  Nat Methods       Date:  2011-05-27       Impact factor: 28.547

3.  Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq.

Authors:  Saiful Islam; Una Kjällquist; Annalena Moliner; Pawel Zajac; Jian-Bing Fan; Peter Lönnerberg; Sten Linnarsson
Journal:  Genome Res       Date:  2011-05-04       Impact factor: 9.043

4.  BamTools: a C++ API and toolkit for analyzing and managing BAM files.

Authors:  Derek W Barnett; Erik K Garrison; Aaron R Quinlan; Michael P Strömberg; Gabor T Marth
Journal:  Bioinformatics       Date:  2011-04-14       Impact factor: 6.937

5.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

6.  RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities.

Authors:  Amy K Barczak; James E Gomez; Benjamin B Kaufmann; Ella R Hinson; Lisa Cosimi; Mark L Borowsky; Andrew B Onderdonk; Sarah A Stanley; Devinder Kaur; Kevin F Bryant; David M Knipe; Alexander Sloutsky; Deborah T Hung
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-02       Impact factor: 11.205

7.  An atlas of combinatorial transcriptional regulation in mouse and man.

Authors:  Timothy Ravasi; Harukazu Suzuki; Carlo Vittorio Cannistraci; Shintaro Katayama; Vladimir B Bajic; Kai Tan; Altuna Akalin; Sebastian Schmeier; Mutsumi Kanamori-Katayama; Nicolas Bertin; Piero Carninci; Carsten O Daub; Alistair R R Forrest; Julian Gough; Sean Grimmond; Jung-Hoon Han; Takehiro Hashimoto; Winston Hide; Oliver Hofmann; Atanas Kamburov; Mandeep Kaur; Hideya Kawaji; Atsutaka Kubosaki; Timo Lassmann; Erik van Nimwegen; Cameron Ross MacPherson; Chihiro Ogawa; Aleksandar Radovanovic; Ariel Schwartz; Rohan D Teasdale; Jesper Tegnér; Boris Lenhard; Sarah A Teichmann; Takahiro Arakawa; Noriko Ninomiya; Kayoko Murakami; Michihira Tagami; Shiro Fukuda; Kengo Imamura; Chikatoshi Kai; Ryoko Ishihara; Yayoi Kitazume; Jun Kawai; David A Hume; Trey Ideker; Yoshihide Hayashizaki
Journal:  Cell       Date:  2010-03-05       Impact factor: 41.582

8.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.

Authors:  Bo Li; Colin N Dewey
Journal:  BMC Bioinformatics       Date:  2011-08-04       Impact factor: 3.307

9.  Differential expression analysis for sequence count data.

Authors:  Simon Anders; Wolfgang Huber
Journal:  Genome Biol       Date:  2010-10-27       Impact factor: 13.583

10.  Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Authors:  Joshua Z Levin; Moran Yassour; Xian Adiconis; Chad Nusbaum; Dawn Anne Thompson; Nir Friedman; Andreas Gnirke; Aviv Regev
Journal:  Nat Methods       Date:  2010-08-15       Impact factor: 28.547
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  104 in total

1.  Total RNA-seq to identify pharmacological effects on specific stages of mRNA synthesis.

Authors:  Sarah A Boswell; Andrew Snavely; Heather M Landry; L Stirling Churchman; Jesse M Gray; Michael Springer
Journal:  Nat Chem Biol       Date:  2017-03-06       Impact factor: 15.040

2.  High-accuracy determination of internal circadian time from a single blood sample.

Authors:  Nicole Wittenbrink; Bharath Ananthasubramaniam; Mirjam Münch; Barbara Koller; Bert Maier; Charlotte Weschke; Frederik Bes; Jan de Zeeuw; Claudia Nowozin; Amely Wahnschaffe; Sophia Wisniewski; Mandy Zaleska; Osnat Bartok; Reut Ashwal-Fluss; Hedwig Lammert; Hanspeter Herzel; Michael Hummel; Sebastian Kadener; Dieter Kunz; Achim Kramer
Journal:  J Clin Invest       Date:  2018-08-06       Impact factor: 14.808

3.  Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.

Authors:  Sofia A Quinodoz; Noah Ollikainen; Barbara Tabak; Ali Palla; Jan Marten Schmidt; Elizabeth Detmar; Mason M Lai; Alexander A Shishkin; Prashant Bhat; Yodai Takei; Vickie Trinh; Erik Aznauryan; Pamela Russell; Christine Cheng; Marko Jovanovic; Amy Chow; Long Cai; Patrick McDonel; Manuel Garber; Mitchell Guttman
Journal:  Cell       Date:  2018-06-07       Impact factor: 41.582

4.  Scalable and cost-effective ribonuclease-based rRNA depletion for transcriptomics.

Authors:  Yiming Huang; Ravi U Sheth; Andrew Kaufman; Harris H Wang
Journal:  Nucleic Acids Res       Date:  2020-02-28       Impact factor: 16.971

5.  Better together: multiplexing samples to improve the preparation and reliability of gene expression studies.

Authors:  Ali Mortazavi
Journal:  Nat Methods       Date:  2015-04       Impact factor: 28.547

6.  Impact of Species Diversity on the Design of RNA-Based Diagnostics for Antibiotic Resistance in Neisseria gonorrhoeae.

Authors:  Crista B Wadsworth; Mohamad R A Sater; Roby P Bhattacharyya; Yonatan H Grad
Journal:  Antimicrob Agents Chemother       Date:  2019-07-25       Impact factor: 5.191

7.  Characterizing Genetic Parts and Devices Using RNA Sequencing.

Authors:  Deepti Vipin; Zoya Ignatova; Thomas E Gorochowski
Journal:  Methods Mol Biol       Date:  2021

Review 8.  Cross-species RNA-seq for deciphering host-microbe interactions.

Authors:  Alexander J Westermann; Jörg Vogel
Journal:  Nat Rev Genet       Date:  2021-02-17       Impact factor: 53.242

9.  A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols.

Authors:  Vayu Maini Rekdal; Paola Nol Bernadino; Michael U Luescher; Sina Kiamehr; Chip Le; Jordan E Bisanz; Peter J Turnbaugh; Elizabeth N Bess; Emily P Balskus
Journal:  Elife       Date:  2020-02-18       Impact factor: 8.140

10.  Structure of the Mucosal and Stool Microbiome in Lynch Syndrome.

Authors:  Yan Yan; David A Drew; Arnold Markowitz; Jason Lloyd-Price; Galeb Abu-Ali; Long H Nguyen; Christina Tran; Daniel C Chung; Katherine K Gilpin; Dana Meixell; Melanie Parziale; Madeline Schuck; Zalak Patel; James M Richter; Peter B Kelsey; Wendy S Garrett; Andrew T Chan; Zsofia K Stadler; Curtis Huttenhower
Journal:  Cell Host Microbe       Date:  2020-04-01       Impact factor: 21.023
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