show Abstracthide AbstractRNA-seq analysis was performed on poly(A) RNA from D. melanogaster treated with various chemicals through feeding, subjected to temperature shock, or exposure to viruses. Total RNA was isolated by the Peter Cherbas group. Isolation of poly(A) RNA and strand-specific library construction were performed in the Brenton Graveley lab. Libraries were distributed among 3 labs in the Drosophila Transcriptome group for sequencing (Celniker, Gingeras, and Graveley) for paired-end RNA sequencing (2x76 nt) on the GAIIx and HiSeq platforms. Fastq files were generated using pipeline version 1.5. Reads were aligned to the genome and a splice-junction database using Bowtie 0.12.0-beta1 and SPA5.pl (to identify only uniquely-mapped reads).