Dataset Information

The developmental transcriptome of Drosophila melanogaster.

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.

SUBMITTER: Graveley BR

PROVIDER: S-EPMC3075879 | biostudies-literature | 2011 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The developmental transcriptome of Drosophila melanogaster.

Graveley Brenton R BR Brooks Angela N AN Carlson Joseph W JW Duff Michael O MO Landolin Jane M JM Yang Li L Artieri Carlo G CG van Baren Marijke J MJ Boley Nathan N Booth Benjamin W BW Brown James B JB Cherbas Lucy L Davis Carrie A CA Dobin Alex A Li Renhua R Lin Wei W Malone John H JH Mattiuzzo Nicolas R NR Miller David D Sturgill David D Tuch Brian B BB Zaleski Chris C Zhang Dayu D Blanchette Marco M Dudoit Sandrine S Eads Brian B Green Richard E RE Hammonds Ann A Jiang Lichun L Kapranov Phil P Langton Laura L Perrimon Norbert N Sandler Jeremy E JE Wan Kenneth H KH Willingham Aarron A Zhang Yu Y Zou Yi Y Andrews Justen J Bickel Peter J PJ Brenner Steven E SE Brent Michael R MR Cherbas Peter P Gingeras Thomas R TR Hoskins Roger A RA Kaufman Thomas C TC Oliver Brian B Celniker Susan E SE

Nature 20101222 7339

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 ...[more]

PMID: 21179090

Similar Datasets

Project description:BackgroundThe formation of matured and individual sperm involves a series of molecular and spectacular morphological changes of the developing cysts in Drosophila melanogaster testis. Recent advances in RNA Sequencing (RNA-Seq) technology help us to understand the complexity of eukaryotic transcriptomes by dissecting different tissues and developmental stages of organisms. To gain a better understanding of cellular differentiation of spermatogenesis, we applied RNA-Seq to analyse the testis-specific transcriptome, including coding and non-coding genes.ResultsWe isolated three different parts of the wild-type testis by dissecting and cutting the different regions: 1.) the apical region, which contains stem cells and developing spermatocytes 2.) the middle region, with enrichment of meiotic cysts 3.) the basal region, which contains elongated post-meiotic cysts with spermatids. Total RNA was isolated from each region and analysed by next-generation sequencing. We collected data from the annotated 17412 Drosophila genes and identified 5381 genes with significant transcript accumulation differences between the regions, representing the main stages of spermatogenesis. We demonstrated for the first time the presence and region specific distribution of 2061 lncRNAs in testis, with 203 significant differences. Using the available modENCODE RNA-Seq data, we determined the tissue specificity indices of Drosophila genes. Combining the indices with our results, we identified genes with region-specific enrichment in testis.ConclusionBy multiple analyses of our results and integrating existing knowledge about Drosophila melanogaster spermatogenesis to our dataset, we were able to describe transcript composition of different regions of Drosophila testis, including several stage-specific transcripts. We present searchable visualizations that can facilitate the identification of new components that play role in the organisation and composition of different stages of spermatogenesis, including the less known, but complex regulation of post-meiotic stages.

Dataset Information

The developmental transcriptome of Drosophila melanogaster.

Publications

The developmental transcriptome of Drosophila melanogaster.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets