Journal article

Improved definition of the mouse transcriptome via targeted RNA sequencing

Giovanni Bussotti, Tommaso Leonardi, Michael B Clark, Tim R Mercer, Joanna Crawford, Lorenzo Malquori, Cedric Notredame, Marcel E Dinger, John S Mattick, Anton J Enright

GENOME RESEARCH | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2016

Abstract

Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand..

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University of Melbourne Researchers

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 Australian National Health and Medical Research Council (NHMRC) Project Grant


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.); an Australian National Health and Medical Research Council (NHMRC) Project Grant (APP1062106 to T.R.M.) and Career Development Fellowship (APP1062470 to T.R.M); 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. We thank Dr. Nilesh Bokil for assistance with mouse dissections; we also thank Dr. Lin Shin, Dr. Anamaria Necsulea, and Dr. Brian Gloss for the useful email communications.