Reference
Citation
Graveley, B.R., Brooks, A.N., Carlson, J.W., Duff, M.O., Landolin, J.M., Yang, L., Artieri, C.G., van Baren, M.J., Boley, N., Booth, B.W., Brown, J.B., Cherbas, L., Davis, C.A., Dobin, A., Li, R., Lin, W., Malone, J.H., Mattiuzzo, N.R., Miller, D., Sturgill, D., Tuch, B.B., Zaleski, C., Zhang, D., Blanchette, M., Dudoit, S., Eads, B., Green, R.E., Hammonds, A., Jiang, L., Kapranov, P., Langton, L., Perrimon, N., Sandler, J.E., Wan, K.H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P.J., Brenner, S.E., Brent, M.R., Cherbas, P., Gingeras, T.R., Hoskins, R.A., Kaufman, T.C., Oliver, B., Celniker, S.E. (2011). The developmental transcriptome of Drosophila melanogaster.  Nature 471(7339): 473--479.
FlyBase ID
FBrf0213330
Publication Type
Research paper
Abstract
Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.
PubMed ID
PubMed Central ID
PMC3075879 (PMC) (EuropePMC)
Related Publication(s)
Personal communication to FlyBase
Total entropy scores for the 67,317 modENCODE junctions.
Graveley, 2011.11.3, Total entropy scores for the 67,317 modENCODE junctions. [FBrf0216691]
Additional low confidence modENCODE junctions.
Graveley, 2011.11.3, Additional low confidence modENCODE junctions. [FBrf0217580]
modENCODE RNA-Seq data remapped to BDGP Release 6 genome assembly.
Brown et al., 2014.8.27, Nature: [FBrf0226107]
modENCODE RNA-Seq junction data
Graveley, 2011.1.5, modENCODE RNA-Seq junction data [FBrf0212682]
The D. melanogaster transcriptome: modENCODE RNA-Seq data
Graveley et al., 2010.03.15, The D. melanogaster transcriptome: modENCODE RNA-Seq data [FBrf0210195]
FlyBase analysis
Analysis and update of genes grouped into 20 co-expression clusters by the modENCODE Transcriptome Group.
FlyBase Genome Annotators, 2011, Analysis and update of genes grouped into 20 co-expression clusters by the modENCODE Transcriptome Group. [FBrf0214296]
Note
Molecular biology: A fly in the face of genomics.
Furlong, 2011, Nature 471(7339): 458--459 [FBrf0214306]
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Nature
    Title
    Nature
    Publication Year
    1869-
    ISBN/ISSN
    0028-0836
    Data From Reference