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Sample GSM2150220 Query DataSets for GSM2150220
Status Public on May 11, 2017
Title pten.Tg.3
Sample type SRA
 
Source name Mouse prostate
Organism Mus musculus
Characteristics tissue type: prostate
pten: WT
trap1: transgenic
replicate: 3
Treatment protocol Twelve RNA samples extracted from Tg prostates were first treated with Invitrogen/Ambion DNA-free-kit (cat #AM1906) to remove DNA
Growth protocol A Pten heterozygous male mouse (http://www.ncbi.nlm.nih.gov/pubmed/9990064) was used in a breeding pair with a TRAP1 transgenic female mouse (line 810). Of the resulting offspring, 25% of the animals were used for further experiments (PTen het-Tg male mice constituted the experimental group, while PTen het-non Tg male mice were used as control group)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol
The sequencing libraries were generated using the Lexogen QuantSeq 3’ mRNA sequencing library preparation kit (SKU:015.24) for Illumina sequencing platform compatible libraries. All 12 libraries were pooled in equal molar amounts and run on the Illumina Nextseq500 using the Mid Output V2 (150 cycles) kit (cat # FC-404-2001)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description RNA-seq for pten WT mouse, transgenic Trap1 replicate 3
Data processing RNA-Seq data analysis was done with rsem(ver. 1.2.3) and mm10 genome with UCSC known gene set.
Two samples were removed as technical outliers based on Principal Component Analysis.
DESeq2 was used for differential expression was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed file contains raw counts for all genes
 
Submission date May 11, 2016
Last update date May 15, 2019
Contact name Priyankara J Wickramasinghe
E-mail(s) priyaw@wistar.org
Phone 2154956837
Organization name The Wistar Institute
Department Bioinformatics
Lab Genomics
Street address 3601 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL19057
Series (1)
GSE81316 Transgenic Expression Of Mitochondrial Chaperone Trap1 Accelerates Prostate Cancer Development
Relations
BioSample SAMN04978793
SRA SRX1756483

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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