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Graveley, B.R., Brooks, A.N., Carlson, J.W., Cherbas, L., Choi, J., Davis, C.A., Dobin, A., Duff, M., Eads, B., Hansen, K.D., Landolin, J., Langton, L., Malone, J., Miller, D., Roberts, J., Sandler, J., Sturgill, D., Tang, H., van Baren, M.J., Wan, K.H., Xiao, S., Yang, L., Zhang, D., Zhang, Y., Zou, Y., Andrews, J., Brenner, S.E., Brent, M., Cherbas, P., Dudoit, S., Gingeras, T.R., Hoskins, R., Kaufman, T., Oliver, B, Celniker, S.E. (2010.03.15). The D. melanogaster transcriptome: modENCODE RNA-Seq data
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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).
Related Publication(s)
Research paper

The developmental transcriptome of Drosophila melanogaster.
Graveley et al., 2011, Nature 471(7339): 473--479 [FBrf0213330]

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