Author affiliations:
1. Graveley, Brooks, Duff, Yang: Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington, Connecticut 06030
2. Andrews, L. Cherbas, P. Cherbas, Kaufman, Miller: Department of Biology, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405
3. Andrews, L. Cherbas, P. Cherbas, Choi, Eads, Roberts, Tang, Xiao, Zhang, Zou: Center for Genomics and Bioinformatics, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405
4. Tang: School of Informatics, Indiana University, 1001 E. 3rd Street, Bloomington, Indiana 47405
5. Brenner: Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
6. Carlson, Celniker, Hoskins, Landolin, Sandler, Wan: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720
7. Davis, Dobin, Gingeras: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 and Affymetrix Inc, Santa Clara, California 95051
8. Dudoit, Hansen: Division of Biostatistics, School of Public Health, University of California, Berkeley, California 94720
9. Brent, Langton, van Baren: Center for Genome Sciences and Department of Computer Science, Washington University, St Louis, MO
10. Malone, Oliver, Sturgill, Zhang: Developmental Genomics Section, NIDDK, National Institutes of Health, Bethesda, MD 20892. 

RNA-seq analysis was performed on poly(A)+ RNA from 30 developmental stages spanning the life cycle of D. melanogaster, from 0-2hr embryos through 30-day male and female adults. Total RNA was isolated by the Peter Cherbas group. Isolation of poly(A)+ RNA and library construction were performed in the Brenton Graveley lab. Libraries were distributed among 5 labs in the Drosophila Transcriptome group for sequencing. The Susan Celniker lab performed paired-end sequencing exclusively (2x76 nt) . The Brenton Graveley, Tom Gingeras and Michael Brent labs performed single-end sequencing exclusively (1x76 and 1x75 nt). The Brian Oliver lab performed both single- and paired-end sequencing. All labs used the same Illumina GAII platform and called bases using the Illumina processing pipeline. Fastq files were generated using pipeline version 1.3 before 5/07/09 and using version 1.4 after that date. Reads were aligned to the genome sequence using either Tophat v.1.0.10 (to identify multiply-mapped reads) OR were aligned to the genome and a splice-junction database using Bowtie 0.9.9 (to identify only uniquely-mapped reads).