TY  - JOUR
A1  - Bussotti, Giovanni
A1  - Leonardi, Tommaso
A1  - Clark, Michael B.
A1  - Mercer, Tim R.
A1  - Crawford, Joanna
A1  - Malquori, Lorenzo
A1  - Notredame, Cedric
A1  - Dinger, Marcel E.
A1  - Mattick, John S.
A1  - Enright, Anton J.
T1  - Improved definition of the mouse transcriptome via targeted RNA sequencing
Y1  - 2016/05/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 705 
EP  - 716 
DO  - 10.1101/gr.199760.115 
VL  - 26 
IS  - 5 
UR  - http://genome.cshlp.org/content/26/5/705.abstract 
N2  - 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 transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources. 
ER  -