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| Status |
Public on Nov 27, 2020 |
| Title |
piRNA analysis of tudor[1] mutant Drosophila brain and ovaries |
| Organism |
Drosophila melanogaster |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
23-29 nt Piwi-interacting RNAs (piRNAs) are crucial components of the ribonucleoprotein complexes which silence the most abundant class of mobile genetic elements in human genome, retrotransposons, in germline (germ) cells. In these cells, antisense piRNAs serve as RNA guides for Piwi proteins, base pairing with transposon RNAs which are subsequently cleaved by Piwi proteins. Germ cells belong to special class of stem cells which ultimately give rise to eggs and sperm and therefore, to next generations. Therefore, piRNAs protect next-generation genomes from devastating mutations caused by transposon insertions. Although, role of piRNAs in germ cells has been studied, functions of piRNAs and their associated proteins in somatic cells are not well understood. Importantly, Piwi proteins are expressed in the fruit fly Drosophila brain and are required for the silencing of transposable elements there, clearly indicating that Piwi-associated piRNAs are involved in this process in the brain. Furthermore, piRNAs have been implicated in the memory formation mechanisms in Aplysia brain. In addition to Piwi proteins, their associated partner, molecular scaffold Tudor protein, participates in piRNA biogenesis in germ cells and it is absolutely required for germline development. However, although tudor gene is expressed in the fly brain, its role in the central nervous system is not understood. In this study, we look at the role of Tudor as an essential player in piRNA biogenesis in Drosophila brain.
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| Overall design |
A total of five brain samples (2 biological replicates for tudor (tud) mutant and 3 biological replicates for wild-type control) and 6 ovarian samples (3 biological replicates for tud mutant and 3 biological replicates for wild-type control) were sequenced for small RNAs, including miRNAs and piRNAs.
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| Contributor(s) |
Tindell SJ, Rouchka EC, Arkov AL |
| Citation(s) |
33219296 |
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| Submission date |
May 01, 2020 |
| Last update date |
Nov 27, 2020 |
| Contact name |
Eric Christian Rouchka |
| E-mail(s) |
[email protected]
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| Organization name |
University of Louisville
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| Department |
Biochemistry and Molecular Genetics
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| Lab |
KY INBRE Bioinformatics Core
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| Street address |
522 East Gray Street
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| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
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| Platforms (1) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (11)
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| GSM4511749 |
Mutant Tudor ovary, small RNA, replicate 1 |
| GSM4511750 |
Mutant Tudor ovary, small RNA, replicate 2 |
| GSM4511751 |
Mutant Tudor ovary, small RNA, replicate 3 |
| GSM4511752 |
Wild-type ovary, small RNA, replicate 1 |
| GSM4511753 |
Wild-type ovary, small RNA, replicate 2 |
| GSM4511754 |
Wild-type ovary, small RNA, replicate 3 |
| GSM4511755 |
Mutant Tudor brain, small RNA, replicate 1 |
| GSM4511756 |
Mutant Tudor brain, small RNA, replicate 2 |
| GSM4511757 |
Wild-type brain, small RNA, replicate 1 |
| GSM4511758 |
Wild-type brain, small RNA, replicate 2 |
| GSM4511759 |
Wild-type brain, small RNA, replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE149750 |
piRNA and transcriptomic analysis of tudor[1] mutant Drosophila brain and ovaries |
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| Relations |
| BioProject |
PRJNA629836 |
| SRA |
SRP259954 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE149748_BRAIN_piRNA_COUNTS_MATRIX_otherRNAsRemoved.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE149748_OVARY_piRNA_COUNTS_MATRIX_otherRNAsRemoved.txt.gz |
15.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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