Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Michael B Clark; Tim R Mercer; Giovanni Bussotti; Tommaso Leonardi; Katelin R Haynes; Joanna Crawford; Marion E Brunck; Kim-Anh Lê Cao; Gethin P Thomas; Wendy Y Chen; Ryan J Taft; Lars K Nielsen; Anton J Enright; John S Mattick; Marcel E Dinger

doi:10.1038/nmeth.3321

Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing

Nat Methods. 2015 Apr;12(4):339-42. doi: 10.1038/nmeth.3321. Epub 2015 Mar 9.

Authors

Affiliations

¹ 1] Garvan Institute of Medical Research, Sydney, Australia. [2] MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK.
² 1] Garvan Institute of Medical Research, Sydney, Australia. [2] St Vincents Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.
³ European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.
⁴ The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia.
⁵ Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
⁶ Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.
⁷ 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.
⁸ 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.

PMID: 25751143
DOI: 10.1038/nmeth.3321

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling*
Humans
K562 Cells
Polymerase Chain Reaction
RNA / blood
RNA / chemistry
RNA / genetics*
RNA, Long Noncoding / genetics*
Sequence Analysis / methods*

Substances

RNA, Long Noncoding
RNA

Associated data

GEO/GSE52503
GEO/GSE61474