Transcriptomics

Dataset Information

297

The Drosophila melanogaster Transcriptome by Paired-End RNA-Sequencing


ABSTRACT: RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100bp paired-end reads were generated on the Illumina GA II yielding 356x sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation. Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites. Poly(A)+ transcripts from 10 distinct stages during the live cycle of D. melanogaster were isolated to generated cDNA libraries which were sequenced on the Illumina GA II instrument.

ORGANISM(S): Drosophila melanogaster  

SUBMITTER: Rui Chen   Bryce Daines 

PROVIDER: E-GEOD-24324 | ArrayExpress | 2010-09-23

SECONDARY ACCESSION(S): GSE24324SRP002072PRJNA132851

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

The Drosophila melanogaster transcriptome by paired-end RNA sequencing.

Daines Bryce B   Wang Hui H   Wang Liguo L   Li Yumei Y   Han Yi Y   Emmert David D   Gelbart William W   Wang Xia X   Li Wei W   Gibbs Richard R   Chen Rui R  

Genome research 20101222 2


RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yielding 356× sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel sp  ...[more]

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