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| Status |
Public on Sep 26, 2023 |
| Title |
Dsim.ovary.2 |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Drosophila simulans |
| Characteristics |
tissue: ovary
rrna depletion: RiboPOOL
assembly: d101g,d15genomes,droSim1,GCF_000754195,GCF_016746395
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| Treatment protocol |
N/A
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| Growth protocol |
All Drosophila species were maintained at room temperature on species-specific food.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ovaries from 10-20 flies were dissected in ice-cold PBS and total RNA was extracted using TRIzol. Briefly, ovaries were lysed in TRIzol (Thermo Fisher Scientific), and RNA was phase separated using chloroform (Sigma-Aldrich). Total RNA in the aqueous fraction was precipitated using 100% isopropanol, washed with 70% ethanol, and dissolved in nuclease free water (Invitrogen). Ribosomal RNA was depleted using RiboPOOL (siTOOLs, Biotech) following the manufacturer's protocol. The indicated RiboZero libraries were prepared as previously described (Kneuss et al., 2019, PMID: 31416967).
RNA-seq libraries were produced using NEBNext Ultra Directional Library Prep Kit for Illumina, following the manufacturer’s instructions for rRNA depleted RNA.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Dsim.ovary.SLX-21520-2.1
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| Data processing |
Removal of adators using Trim Galore! (v0.6.4, --stringency 6 -e 0.1).
Alignment to the reference genome using HiSeq2 (v2.2.0, -max-seeds 100 -q -k 1).
Converting to bigWig and scaling to cpm using bamCoverage from deeptools (v3.3.2, --binSize 1 --ignoreForNormalization chrM --normalizeUsing CPM --exactScaling --skipNonCoveredRegions, and additionally --filterRNAstrand and --scaleFactor).
Supplementary files format and content: bigWig showing read coverage per position. File name indicate species, genome assembly, strand, and sample.
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| Submission date |
Feb 22, 2023 |
| Last update date |
Sep 26, 2023 |
| Contact name |
Susanne Bornelöv |
| E-mail(s) |
susanne.bornelov@cruk.cam.ac.uk
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| Organization name |
University of Cambridge
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| Department |
Cancer Research UK - Cambridge Institute
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| Lab |
Hannon
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| Street address |
Robinson Way
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| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
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| Platform ID |
GPL33169 |
| Series (2) |
| GSE225887 |
Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus [RNA-Seq] |
| GSE225889 |
Unistrand piRNA clusters are an evolutionarily conserved mechanism to suppress endogenous retroviruses across the Drosophila genus |
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| Relations |
| BioSample |
SAMN33419372 |
| SRA |
SRX19477723 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7059832_Dsim.GCF_000754195.minus.ovary.SLX-21520-2.uniq.bw |
20.5 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.GCF_000754195.plus.ovary.SLX-21520-2.uniq.bw |
22.3 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.GCF_016746395.minus.ovary.SLX-21520-2.uniq.bw |
19.9 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.GCF_016746395.plus.ovary.SLX-21520-2.uniq.bw |
21.5 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.d101g.minus.ovary.SLX-21520-2.uniq.bw |
19.7 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.d101g.plus.ovary.SLX-21520-2.uniq.bw |
21.8 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.d15genomes.minus.ovary.SLX-21520-2.uniq.bw |
19.7 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.d15genomes.plus.ovary.SLX-21520-2.uniq.bw |
21.6 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.droSim1.minus.ovary.SLX-21520-2.uniq.bw |
18.7 Mb |
(ftp)(http) |
BW |
| GSM7059832_Dsim.droSim1.plus.ovary.SLX-21520-2.uniq.bw |
20.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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