Literature DB >> 25751143

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.

Michael B Clark1, Tim R Mercer2, Giovanni Bussotti3, Tommaso Leonardi3, Katelin R Haynes4, Joanna Crawford5, Marion E Brunck6, Kim-Anh Lê Cao7, Gethin P Thomas4, Wendy Y Chen2, Ryan J Taft8, Lars K Nielsen6, Anton J Enright3, John S Mattick2, Marcel E Dinger2.   

Abstract

We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas.

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Year:  2015        PMID： 25751143     DOI： 10.1038/nmeth.3321

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


  42 in total

Review 1.  Alternative splicing and evolution: diversification, exon definition and function.

Authors:  Hadas Keren; Galit Lev-Maor; Gil Ast
Journal:  Nat Rev Genet       Date:  2010-04-08       Impact factor: 53.242

2.  Synthetic spike-in standards for RNA-seq experiments.

Authors:  Lichun Jiang; Felix Schlesinger; Carrie A Davis; Yu Zhang; Renhua Li; Marc Salit; Thomas R Gingeras; Brian Oliver
Journal:  Genome Res       Date:  2011-08-04       Impact factor: 9.043

3.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.

Authors:  Moran N Cabili; Cole Trapnell; Loyal Goff; Magdalena Koziol; Barbara Tazon-Vega; Aviv Regev; John L Rinn
Journal:  Genes Dev       Date:  2011-09-02       Impact factor: 11.361

4.  Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Authors:  Tim R Mercer; Michael B Clark; Joanna Crawford; Marion E Brunck; Daniel J Gerhardt; Ryan J Taft; Lars K Nielsen; Marcel E Dinger; John S Mattick
Journal:  Nat Protoc       Date:  2014-04-03       Impact factor: 13.491

5.  Targeted RNA sequencing reveals the deep complexity of the human transcriptome.

Authors:  Tim R Mercer; Daniel J Gerhardt; Marcel E Dinger; Joanna Crawford; Cole Trapnell; Jeffrey A Jeddeloh; John S Mattick; John L Rinn
Journal:  Nat Biotechnol       Date:  2011-11-13       Impact factor: 54.908

6.  The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Authors:  Thomas Derrien; Rory Johnson; Giovanni Bussotti; Andrea Tanzer; Sarah Djebali; Hagen Tilgner; Gregory Guernec; David Martin; Angelika Merkel; David G Knowles; Julien Lagarde; Lavanya Veeravalli; Xiaoan Ruan; Yijun Ruan; Timo Lassmann; Piero Carninci; James B Brown; Leonard Lipovich; Jose M Gonzalez; Mark Thomas; Carrie A Davis; Ramin Shiekhattar; Thomas R Gingeras; Tim J Hubbard; Cedric Notredame; Jennifer Harrow; Roderic Guigó
Journal:  Genome Res       Date:  2012-09       Impact factor: 9.043

7.  lncRNAdb: a reference database for long noncoding RNAs.

Authors:  Paulo P Amaral; Michael B Clark; Dennis K Gascoigne; Marcel E Dinger; John S Mattick
Journal:  Nucleic Acids Res       Date:  2010-11-25       Impact factor: 16.971

8.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937

9.  Pfam: the protein families database.

Authors:  Robert D Finn; Alex Bateman; Jody Clements; Penelope Coggill; Ruth Y Eberhardt; Sean R Eddy; Andreas Heger; Kirstie Hetherington; Liisa Holm; Jaina Mistry; Erik L L Sonnhammer; John Tate; Marco Punta
Journal:  Nucleic Acids Res       Date:  2013-11-27       Impact factor: 16.971

10.  Landscape of transcription in human cells.

Authors:  Sarah Djebali; Carrie A Davis; Angelika Merkel; Alex Dobin; Timo Lassmann; Ali Mortazavi; Andrea Tanzer; Julien Lagarde; Wei Lin; Felix Schlesinger; Chenghai Xue; Georgi K Marinov; Jainab Khatun; Brian A Williams; Chris Zaleski; Joel Rozowsky; Maik Röder; Felix Kokocinski; Rehab F Abdelhamid; Tyler Alioto; Igor Antoshechkin; Michael T Baer; Nadav S Bar; Philippe Batut; Kimberly Bell; Ian Bell; Sudipto Chakrabortty; Xian Chen; Jacqueline Chrast; Joao Curado; Thomas Derrien; Jorg Drenkow; Erica Dumais; Jacqueline Dumais; Radha Duttagupta; Emilie Falconnet; Meagan Fastuca; Kata Fejes-Toth; Pedro Ferreira; Sylvain Foissac; Melissa J Fullwood; Hui Gao; David Gonzalez; Assaf Gordon; Harsha Gunawardena; Cedric Howald; Sonali Jha; Rory Johnson; Philipp Kapranov; Brandon King; Colin Kingswood; Oscar J Luo; Eddie Park; Kimberly Persaud; Jonathan B Preall; Paolo Ribeca; Brian Risk; Daniel Robyr; Michael Sammeth; Lorian Schaffer; Lei-Hoon See; Atif Shahab; Jorgen Skancke; Ana Maria Suzuki; Hazuki Takahashi; Hagen Tilgner; Diane Trout; Nathalie Walters; Huaien Wang; John Wrobel; Yanbao Yu; Xiaoan Ruan; Yoshihide Hayashizaki; Jennifer Harrow; Mark Gerstein; Tim Hubbard; Alexandre Reymond; Stylianos E Antonarakis; Gregory Hannon; Morgan C Giddings; Yijun Ruan; Barbara Wold; Piero Carninci; Roderic Guigó; Thomas R Gingeras
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962
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  73 in total

1.  Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage.

Authors:  Joshua A Betts; Mahdi Moradi Marjaneh; Fares Al-Ejeh; Yi Chieh Lim; Wei Shi; Haran Sivakumaran; Romain Tropée; Ann-Marie Patch; Michael B Clark; Nenad Bartonicek; Adrian P Wiegmans; Kristine M Hillman; Susanne Kaufmann; Amanda L Bain; Brian S Gloss; Joanna Crawford; Stephen Kazakoff; Shivangi Wani; Shu W Wen; Bryan Day; Andreas Möller; Nicole Cloonan; John Pearson; Melissa A Brown; Timothy R Mercer; Nicola Waddell; Kum Kum Khanna; Eloise Dray; Marcel E Dinger; Stacey L Edwards; Juliet D French
Journal:  Am J Hum Genet       Date:  2017-08-03       Impact factor: 11.025

Review 2.  Unique features of long non-coding RNA biogenesis and function.

Authors:  Jeffrey J Quinn; Howard Y Chang
Journal:  Nat Rev Genet       Date:  2016-01       Impact factor: 53.242

Review 3.  Characters, functions and clinical perspectives of long non-coding RNAs.

Authors:  Ruifang Wu; Yuwen Su; Haijing Wu; Yong Dai; Ming Zhao; Qianjin Lu
Journal:  Mol Genet Genomics       Date:  2016-02-17       Impact factor: 3.291

Review 4.  Towards a complete map of the human long non-coding RNA transcriptome.

Authors:  Barbara Uszczynska-Ratajczak; Julien Lagarde; Adam Frankish; Roderic Guigó; Rory Johnson
Journal:  Nat Rev Genet       Date:  2018-09       Impact factor: 53.242

5.  Annotation of Full-Length Long Noncoding RNAs with Capture Long-Read Sequencing (CLS).

Authors:  Sílvia Carbonell Sala; Barbara Uszczyńska-Ratajczak; Julien Lagarde; Rory Johnson; Roderic Guigó
Journal:  Methods Mol Biol       Date:  2021

6.  Validation of a Targeted RNA Sequencing Assay for Kinase Fusion Detection in Solid Tumors.

Authors:  Julie W Reeser; Dorrelyn Martin; Jharna Miya; Esko A Kautto; Ezra Lyon; Eliot Zhu; Michele R Wing; Amy Smith; Matthew Reeder; Eric Samorodnitsky; Hannah Parks; Karan R Naik; Joseph Gozgit; Nicholas Nowacki; Kurtis D Davies; Marileila Varella-Garcia; Lianbo Yu; Aharon G Freud; Joshua Coleman; Dara L Aisner; Sameek Roychowdhury
Journal:  J Mol Diagn       Date:  2017-08-09       Impact factor: 5.568

7.  Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations.

Authors:  Dorrelyn P Martin; Jharna Miya; Julie W Reeser; Sameek Roychowdhury
Journal:  J Vis Exp       Date:  2016-08-04       Impact factor: 1.355

8.  Target-enrichment sequencing for detailed characterization of small RNAs.

Authors:  Quan Nguyen; Julio Aguado; Fabio Iannelli; Ana Maria Suzuki; Francesca Rossiello; Fabrizio d'Adda di Fagagna; Piero Carninci
Journal:  Nat Protoc       Date:  2018-03-22       Impact factor: 13.491

Review 9.  Understanding the Role of lncRNAs in Nervous System Development.

Authors:  Brian S Clark; Seth Blackshaw
Journal:  Adv Exp Med Biol       Date:  2017       Impact factor: 2.622

Review 10.  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
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