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Series GSE16960 Query DataSets for GSE16960
Status Public on May 04, 2010
Title Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Summary Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. We identified a set of genes that have sex-specific isoforms in wild-type (WT) gonads, including several transcription factors. We found that differentiation of sperms from undifferentiated germ cells induced a dramatic downregulation of RNA splicing factors. Our data confirmed that RNA splicing events are significantly more frequent in the undifferentiated cell-enriched bag of marbles (bam) mutant testis, but downregulated upon differentiation in WT testis. Consistent with this, we showed that genes required for meiosis and terminal differentiation in WT testis were mainly regulated at the transcriptional level, but not by alternative splicing. Unexpectedly, we observed an increase in expression of all families of chromatin remodeling factors and histone modifying enzymes in the undifferentiated cell-enriched bam testis. More interestingly, chromatin regulators and histone modifying enzymes with opposite enzymatic activities are coenriched in undifferentiated cells in testis, suggesting that these cells may possess dynamic chromatin architecture. Finally, our data revealed many new features of the Drosophila gonadal transcriptomes, and will lead to a more comprehensive understanding of how differential gene expression and splicing regulate gametogenesis in Drosophila. Our data provided a foundation for the systematic study of gene expression and alternative splicing in many interesting areas of germ cell biology in Drosophila, such as the molecular basis for sexual dimorphism and the regulation of the proliferation vs terminal differentiation programs in germline stem cell lineages.
Overall design RNA-Seq experiments for four Drosophila melanogaster samples: (1) bam mutant testes, (2) wild-type testes, (3) bam mutant ovaries, (4) wild-type ovaries
Contributor(s) Gan Q, Chepelev I, Wei G, Tarayrah L, Cui K, Zhao K, Chen X
Citation(s) 20440302, 22019781
Submission date Jul 06, 2009
Last update date May 15, 2019
Contact name Iouri Chepelev
Organization name US Department of Veterans Affairs Medical Center
Street address 3200 Vine St
City Cincinnati
State/province OH
ZIP/Postal code 45220
Country USA
Platforms (1)
GPL9061 Illumina Genome Analyzer II (Drosophila melanogaster)
Samples (4)
GSM424748 Bam mutant testes
GSM424749 Wild type testes
GSM424750 Bam mutant ovaries
SRA SRP001566
BioProject PRJNA117723

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Supplementary file Size Download File type/resource
GSE16960_RAW.tar 2.8 Gb (http)(custom) TAR (of GRAPH, TXT)
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Processed data provided as supplementary file
Raw data are available in SRA

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