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Sample GSM3631052 Query DataSets for GSM3631052
Status Public on Oct 22, 2019
Title WT-2
Sample type SRA
 
Source name wildtype
Organism Drosophila melanogaster
Characteristics strain: wBerlin
tissue: ovary
age: 1-3 days old
Treatment protocol 0-2 day old Drosophila females were collected from actively growing stocks of wildtype or GCNAKO and fed on wet yeast for 24 hours before dissection, collection of ovaries and RNA extraction. All stocks were maintained at room temperature (25°C) and fed on standard feed.
Extracted molecule total RNA
Extraction protocol Used standard protocol from Qiagen miRNEasy kit with on columnb Qiagen DNAse digest to remove and contaminating DNA species.
From the NGS core at UTSouthwestern: Total RNA is depleted of its rRNA and fragmented before strand specific cDNA synthesis. cDNA are then a-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using SBS v3 reagents.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description wildtype
total RNA including small RNA species (18 nt upwards)
Data processing Basecalls were performed using CASAVA (v. 1.8.2)
Reads were aligned to dm6 geneome assembly and transcript assembly was performed using STAR (v.2.5)
Normalized expression calculation and differential expression analysis was performed using DESeq2
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each sample …
 
Submission date Feb 26, 2019
Last update date Oct 22, 2019
Contact name Michael Buszczak
E-mail(s) Michael.Buszczak@UTSouthwestern.edu
Phone 214-648-4941
Organization name University of Texas Southwestern Medical Center
Department Molecular Biology
Lab Buszczak Lab
Street address 5323 Harry Hines Boulevard
City Dallas
State/province Texas
ZIP/Postal code 75390
Country USA
 
Platform ID GPL17275
Series (1)
GSE127220 Sequencing of all RNA species by next generation sequencing of wildtype and GCNAKO Drosophila ovaries
Relations
BioSample SAMN11024185
SRA SRX5433999

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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