Developmental Profile of the Drosophila Transcriptome by Paired-End RNA-Sequencing. Drosophila melanogaster

In order to gain a broad sampling of the Drosophila transcriptome, RNA-Seq experiments were performed at all stages of the Drosophila life cycle, and 12 independent cDNA libraries were generated, including embryonic, larval, pupal, and adult. Some libraries were staged as specific windows: 2-4 hour embryo, 14-16 hour embryo, 3rd instar larva, 3-day pupa, and 17-day adult. Additional libraries were derived from broadly staged mixed samples: embryo, larvae, and pupa. Three-day old male and female adults were sequenced separately for discovery of sex-specific variation. Finally, one library of mixed-age pupal RNA was sequenced in replicate as a validation of the technology. A total of 272 million paired-end reads of 64-75 base pairs in length were obtained, representing greater than 690x sequence coverage of the 30Mb Drosophila melanogaster transcriptome.