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| Status |
Public on Oct 15, 2015 |
| Title |
CG9754_het_rep1_smRNAseq |
| Sample type |
SRA |
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| Source name |
adult fly ovaries
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: ovaries
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| Treatment protocol |
Flies were fed with yeast paste. Germline specific knockdowns were done as described (Czech et al., 2013 Mol Cell).
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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 ovaries of 2-3 day old females of the indicated knockdowns was isolated using TRIzol (Invitrogen).
Small libraries were prepared as described (Czech et al., 2013 Mol Cell).
small RNA cloning (End cloning)
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
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| Description |
small RNA sequencing
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| Data processing |
Demultiplexed, concatenated files with the 50nt or 76nt 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 (dm3) 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). For comparison of small RNA counts between samples, libraries of dsRNA-white samples were set to one million reads. Next, all libraries were normalized based on unique mappers to the flamenco (for nos-GAL4 knockdowns) piRNA clusters.
Genome_build: dm3/2006
Supplementary_files_format_and_content: Excel file contains read counts of small RNAs (24 nt to 29 nt) mapping to antisense transposon consensus normalized to total miRNA reads comparing CG9754 heterozygous and mutant in sheet "het_vs_mut_CG9754". In sheet "untethered_vs_tethered", read counts of small RNAs (24 nt to 29 nt) mapping to piRNA clusters are shown.
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| Submission date |
Jul 27, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yang Yu |
| E-mail(s) |
[email protected]
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| Organization name |
Cold Spring Harbor Laboratory
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| Lab |
Hannon Lab
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| Street address |
One Bungtown Road
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| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL16479 |
| Series (2) |
| GSE71372 |
Panoramix enforces piRNA-dependent co-transcriptional silencing (small RNA-Seq) |
| GSE71374 |
Panoramix enforces piRNA-dependent co-transcriptional silencing |
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| Relations |
| BioSample |
SAMN03939114 |
| SRA |
SRX1120744 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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