@article{Daines01022011,
author = {Daines, Bryce and Wang, Hui and Wang, Liguo and Li, Yumei and Han, Yi and Emmert, David and Gelbart, William and Wang, Xia and Li, Wei and Gibbs, Richard and Chen, Rui}, 
title = {The Drosophila melanogaster transcriptome by paired-end RNA sequencing},
volume = {21}, 
number = {2}, 
pages = {315-324}, 
year = {2011}, 
doi = {10.1101/gr.107854.110}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/21/2/315.abstract}, 
eprint = {http://genome.cshlp.org/content/21/2/315.full.pdf+html}, 
journal = {Genome Research} 
}