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Series GSE44612 Query DataSets for GSE44612
Status Public on Feb 25, 2013
Title Comparative Validation of the D. melanogaster Encyclopedia of DNA Elements Transcript Models
Project modENCODE
Organisms Drosophila ananassae; Drosophila melanogaster; Drosophila mojavensis; Drosophila pseudoobscura; Drosophila simulans; Drosophila virilis; Drosophila yakuba; Drosophila eugracilis; Drosophila takahashii; Drosophila elegans; Drosophila ficusphila; Drosophila kikkawai; Drosophila bipectinata; Drosophila biarmipes; Drosophila rhopaloa
Experiment type Expression profiling by high throughput sequencing
Summary The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function. We have performed RNA-Seq and CAGE-Seq experiments on more than 80 samples from multiple tissues and stages of 15 Drosophila species, including 8 previously unsequenced genomes. We have found strikingly conserved sequence, expression, and splicing for the vast majority of transcript models in modENCODE annotation (e.g. 99% exons of coding sequences (CDS), 88% exons of untranslated regions (UTR), and 87% splicing events), indicating that the transcriptome annotation is of very high quality. We also describe dynamic transcriptome evolution within the Drosophila genus, including conserved promoter structure, labile positions of transcription start sites, and rapidly evolving RNA-editing events. We demonstrate how this phylogenetic approach to DNA element validation will prove useful in the annotation of other high priority genomes, especially for genomes that are less compact than Drosophila (e.g. the vast majority of vertebrate genomes).
Overall design Refer to individual Series (listed below).
Citation(s) 24985915
BioProject PRJNA200701
Submission date Feb 25, 2013
Last update date May 15, 2019
Contact name Brian Oliver
Phone 301-204-9463
Organization name NIDDK, NIH
Department LBG
Lab Developmental Genomics
Street address 50 South Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (34)
GPL9061 Illumina Genome Analyzer II (Drosophila melanogaster)
GPL9395 Illumina Genome Analyzer (Drosophila pseudoobscura)
GPL9958 Illumina Genome Analyzer II (Drosophila pseudoobscura)
Samples (93)
GSM499403 Head_Dpseud_Female
GSM499404 Head_Dpseud_Male
GSM509821 Head_Dmel_Female (GA II)
This SuperSeries is composed of the following SubSeries:
GSE19989 mRNA-Seq of head tissue from Drosophila pseudoobscura
GSE20348 mRNA-Seq of head tissue from Drosophila melanogaster
GSE20882 mRNA-Seq of head tissue from Drosophila mojavensis

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE44612_RAW.tar 129.8 Gb (http)(custom) TAR (of BAM, BED, RPKM, TXT)
SRA Run SelectorHelp

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