Journal article

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 Le Cao, Gethin P Thomas, Wendy Y Chen, Ryan J Taft, Lars K Nielsen, Anton J Enright, John S Mattick, Marcel E Dinger

NATURE METHODS | NATURE PUBLISHING GROUP | Published : 2015

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.

Grants

Awarded by Australian National Health and Medical Research Council (NHMRC) Australia Fellowship


Awarded by NHMRC Early Career Fellowship


Awarded by EMBO Long Term Fellowship


Awarded by Biotechnology and Biological Sciences Research Council


Funding Acknowledgements

The authors acknowledge the following funding sources: an Australian National Health and Medical Research Council (NHMRC) Australia Fellowship (631668 to J.S.M. and 631542 to M.E.D.), an NHMRC Early Career Fellowship (APP1072662 to M.B.C.), an EMBO Long Term Fellowship (ALTF 864-2013 to M.B.C.), the Queensland State Government (National and International Research Alliance Program to L.K.N.) and an EMBL Interdisciplinary Postdoc (EIPOD) under Marie Curie Actions (COFUND) (to G.B.). The contents of the published material are solely the responsibility of the administering institution, a participating institution or individual authors and do not reflect the views of NHMRC. The authors thank the ENCODE consortium for the provision of data; data were employed in strict accordance with the associated data-release policy. The authors also thank Prof. M. Brown (University of Queensland) for contributions to manuscript preparation.