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| Status |
Public on Oct 15, 2019 |
| Title |
Defining the Expression of piRNAs and Transposable Elements in Drosophila Ovarian Germline Stem Cells and Niche Cells |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Summary: Piwi-interacting RNAs (piRNAs) are important for repressing transposable elements (TEs) and modulating gene expression in germ cells, thereby maintaining genome stability and germ cell function. Here, we show that the canonical piRNA clusters are more active in GSCs (germline stem cells) and their early progeny than late germ cells, and identify new piRNA clusters using deep RNA sequencing. We show that GSCs have higher piRNA levels and lower TE levels than niche cells. Furthermore, many mRNA 3’UTR also exhibit the production of sense, antisense or dual-stranded piRNA. Finally, we show that there are extensive differences in alternative promoter usage and splicing which are likely to modulate gene function in GSCs and niche cells. Overall, this study serves as a major resource for the investigation of piRNA and TE dynamics in GSCs and niche cells.
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| Overall design |
RNA-seq experiments isolating mRNA and smallRNA were performed for bam/bgcn/tkv, mutant ovaries and wildtype ovaries. The same type of sequencing was subsequently performed on GSCs and their surrounding niche cells.
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| Contributor(s) |
Story B, Ma X, Ishihara K, Blanchette M, Li H, Hall K, Peak A, Anoja P, Park J, Haug J, Xie T |
| Citation(s) |
31619466 |
| Submission date |
Sep 12, 2018 |
| Last update date |
Oct 21, 2019 |
| Contact name |
Benjamin Andrew Story |
| E-mail(s) |
story.benjamin@gmail.com
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| Organization name |
European Molecular Biology Laboratory (EMBL)
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| Department |
Genomics
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| Street address |
Meyerhofstrasse 1
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| City |
Heidelberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
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| Platforms (1) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
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| Samples (57)
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| Relations |
| BioProject |
PRJNA490506 |
| SRA |
SRP161577 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119862_GSC_vs_SC_DGE.xls.gz |
377.1 Kb |
(ftp)(http) |
XLS |
| GSE119862_bam_vs_WT_DGE.xls.gz |
378.2 Kb |
(ftp)(http) |
XLS |
| GSE119862_bgcn_vs_WT_DGE.xls.gz |
378.3 Kb |
(ftp)(http) |
XLS |
| GSE119862_new_clusters.bed.gz |
39.3 Kb |
(ftp)(http) |
BED |
| GSE119862_tkvM1_vs_WT_DGE.xls.gz |
378.4 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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