RT Journal
A1 Daines, Bryce
A1 Wang, Hui
A1 Wang, Liguo
A1 Li, Yumei
A1 Han, Yi
A1 Emmert, David
A1 Gelbart, William
A1 Wang, Xia
A1 Li, Wei
A1 Gibbs, Richard
A1 Chen, Rui
T1 The Drosophila melanogaster transcriptome by paired-end RNA sequencing
JF Genome Research 
JO Genome Research 
YR 2011 
FD February 01 
VO 21 
IS 2 
SP 315 
OP 324 
DO 10.1101/gr.107854.110 
UL http://genome.cshlp.org/content/21/2/315.abstract 
AB RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64–100-bp paired-end reads were generated on the Illumina GA II yielding 356× sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation. Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites.