Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
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.
1] Garvan Institute of Medical Research, Sydney, Australia. [2] MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK.
Michael B
0000000229039537
MB
Clark
1] Garvan Institute of Medical Research, Sydney, Australia. [2] St Vincents Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.
Tim R
TR
Mercer
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
Giovanni
G
Bussotti
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
Tommaso
T
Leonardi
The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia.
Katelin R
KR
Haynes
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
Joanna
J
Crawford
Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.
Marion E
ME
Brunck
1] The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia. [2] Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
Kim-Anh Lê
KA
Cao
The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia.
Gethin P
GP
Thomas
1] Garvan Institute of Medical Research, Sydney, Australia. [2] St Vincents Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.
Wendy Y
WY
Chen
1] Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia. [2] Illumina, Inc., San Diego, California, USA. [3] School of Medicine and Health Services, Departments of Integrated Systems Biology and Pediatrics, George Washington University, Washington DC, USA.
Ryan J
RJ
Taft
Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.
Lars K
0000000181913511
LK
Nielsen
European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
Anton J
AJ
Enright
1] Garvan Institute of Medical Research, Sydney, Australia. [2] St Vincents Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.
John S
0000000276807527
JS
Mattick
1] Garvan Institute of Medical Research, Sydney, Australia. [2] St Vincents Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.
Marcel E
ME
Dinger
D020869:Gene Expression Profiling; D006801:Humans; D020014:K562 Cells; D016133:Polymerase Chain Reaction; D012313:RNA / Q000097:blood / Q000737:chemistry / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D017421:Sequence Analysis / Q000379:methods*
D062085:RNA, Long Noncoding; D012313:RNA