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| Status |
Public on May 31, 2012 |
| Title |
1day_old_testes |
| Sample type |
SRA |
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| Source name |
D. melanogaster testes_1 day
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Wild-type flies (Oregon R)
tissue: testes
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| Treatment protocol |
Aging paradigm was used as described previously (Boyle et al., 2007).
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| Growth protocol |
Flies were raised at 25°C on standard cornmeal-molasses agar medium.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from testes of 1005 (1-day) and 1018 (30-day) old wild-type (OreR) males was isolated using TRIzol (Invitrogen). 19- to 28-nt small RNAs were cloned as described (Brennecke et al., 2007).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
small RNA sequencing
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| Data processing |
The 36nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome using nexalign. Only reads that met these conditions were subjected to further analyses.
For annotations we used a combination of UCSC [dm3], miRBase [release 14], and Flybase [r5.26] tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request).
Genome_build: dm3
Supplementary_files_format_and_content: txt files contain genome-matching small RNA sequences, read lengths, annotation names and read counts. Formate: SEQ = the sequence of the small RNA. LENGTH = the length of the small RNA. NAME = annotation name of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.
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| Submission date |
Apr 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin Czech |
| E-mail(s) |
czech@cshl.edu
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| Organization name |
Cold Spring Harbor Laboratory
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| Lab |
Hannon
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| Street address |
1 Bungtown Rd
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| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL9061 |
| Series (1) |
| GSE37041 |
The let-7-Imp axis regulates aging of the Drosophila testis stem cell niche. |
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| Relations |
| Reanalyzed by |
GSM3277328 |
| SRA |
SRX135547 |
| BioSample |
SAMN00849467 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM909277_1day_old_testes.txt.gz |
21.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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