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The developmental transcriptome of Drosophila melanogaster.

Nature | Mar 24, 2011

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: 21179090 RIS Download

Mesh terms: Alternative Splicing | Animals | Base Sequence | Drosophila Proteins | Drosophila melanogaster | Exons | Female | Gene Expression Profiling | Gene Expression Regulation, Developmental | Genes, Insect | Genome, Insect | Male | MicroRNAs | Oligonucleotide Array Sequence Analysis | Protein Isoforms | RNA Editing | RNA, Messenger | RNA, Small Untranslated | Sequence Analysis | Sex Characteristics | Transcription, Genetic

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Associated grants

  • Agency: NHGRI NIH HHS, Id: U01 HG004271
  • Agency: NHGRI NIH HHS, Id: U01 HG004271-01
  • Agency: Howard Hughes Medical Institute, Id: ZIA DK015600-14
  • Agency: Intramural NIH HHS, Id: U01 HB004271
  • Agency: NHLBI NIH HHS, Id:

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modENCODE

A comprehensive encyclopedia of genomic functional elements in the model organisms C. elegans and D. melanogaster. modENCODE is run as a Research Network and the consortium is formed by 11 primary projects, divided between worm and fly, spanning the domains of gene structure, mRNA and ncRNA expression profiling, transcription factor binding sites, histone modifications and replacement, chromatin structure, DNA replication initiation and timing, and copy number variation. The raw and interpreted data from this project is vetted by a data coordinating center (DCC) to ensure consistency and completeness. The entire modENCODE data corpus is now available on the Amazon Web Services EC2 cloud. What this means is that virtual machines and virtual compute clusters that you run within the EC2 cloud can mount the modENCODE data set in whole or in part. Your software can run analyses against the data files directly without experiencing the long waits and logistics associated with copying the datasets over to your local hardware. You may also view the data using GBrowse, Dataset Search, or download the data via FTP, as well as download pre-release datasets.

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