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| Status |
Public on May 30, 2018 |
| Title |
Twin-miRs and their many weak targets |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNAs (miRNA) are small, endogenous RNAs that regulate the expression of mRNAs posttranscriptionally. To identify miRNAs that produce twin products, we sequenced these five small RNA libraries and collected other published datasets to represent a systematic coverage of the major tissue types (head, body and sexual organs) in D. melanogaster. To survey the repression effects of twin miRs on the their targets, we dissected testes from adult flies that lacked Dm310s due to a knock-out mutation (Tang, et al. 2010) and performed an RNA-seq analysis.
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| Overall design |
Five small RNA samples mainly from reproductive organs, and four RNA-seq samples from testes, were analyzed in D. melanogaster.
Please note that the 'CanS testes' raw data fastq file is unavailable and only fasta file containing clean reads and read counts was generated as following; the sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and collapsed to the fasta format, on which the further analysis was carried out.
The Gene_Expression_log2(RPKM).txt contains two additional data columns - miR-313-3p_target and miR-313-5p_target - showing whether it is a TargetScan predicted target of dme-miR-313-3p or -5p, respectively.
Both 'Dm310s mutant' and 'Control' flies are generated from the stock EP(2)2587 [P(3)l(2)05510EP2587; Szeged Stock Center)]. The detailed construction method is described in Tang, T., et al. (2010; PMID 20615957)
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| Contributor(s) |
Zhao Y, Lin P, Liufu Z, Yang H, Lyu Y, Shen X, Wu C, Tang T |
| Citation(s) |
29688430 |
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| Submission date |
Apr 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yixin Zhao |
| E-mail(s) |
[email protected]
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| Organization name |
Cold Spring Harbor Laboratory
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| Street address |
1 Bungtown Road
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| City |
Cold Spring Harbor |
| State/province |
NEW YORK |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platforms (2) |
| GPL9061 |
Illumina Genome Analyzer II (Drosophila melanogaster) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA381503 |
| SRA |
SRP102964 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE97364_Gene_Expression_log2_RPKM_.txt.gz |
186.8 Kb |
(ftp)(http) |
TXT |
| GSE97364_RAW.tar |
82.8 Mb |
(http)(custom) |
TAR (of FA) |
| GSE97364_miRNA_expression.xlsx |
58.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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