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Sample GSM7059813 Query DataSets for GSM7059813
Status Public on Sep 26, 2023
Title Dere.ovary.2
Sample type SRA
 
Source name ovary
Organism Drosophila erecta
Characteristics tissue: ovary
rrna depletion: RiboPOOL
assembly: d101g,d15genomes,droEre1,GCF_003286155
Treatment protocol N/A
Growth protocol All Drosophila species were maintained at room temperature on species-specific food.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Dere.ovary.SLX-21520-2.1
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.
 
Submission date Feb 22, 2023
Last update date Sep 26, 2023
Contact name Susanne Bornelöv
E-mail(s) susanne.bornelov@cruk.cam.ac.uk
Organization name University of Cambridge
Department Cancer Research UK - Cambridge Institute
Lab Hannon
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL33164
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
Relations
BioSample SAMN33419391
SRA SRX19477704

Supplementary file Size Download File type/resource
GSM7059813_Dere.GCF_003286155.minus.ovary.SLX-21520-2.uniq.bw 22.9 Mb (ftp)(http) BW
GSM7059813_Dere.GCF_003286155.plus.ovary.SLX-21520-2.uniq.bw 23.7 Mb (ftp)(http) BW
GSM7059813_Dere.d101g.minus.ovary.SLX-21520-2.uniq.bw 22.8 Mb (ftp)(http) BW
GSM7059813_Dere.d101g.plus.ovary.SLX-21520-2.uniq.bw 24.0 Mb (ftp)(http) BW
GSM7059813_Dere.d15genomes.minus.ovary.SLX-21520-2.uniq.bw 25.4 Mb (ftp)(http) BW
GSM7059813_Dere.d15genomes.plus.ovary.SLX-21520-2.uniq.bw 23.4 Mb (ftp)(http) BW
GSM7059813_Dere.droEre1.minus.ovary.SLX-21520-2.uniq.bw 23.0 Mb (ftp)(http) BW
GSM7059813_Dere.droEre1.plus.ovary.SLX-21520-2.uniq.bw 24.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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