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Sample GSM3543703 Query DataSets for GSM3543703
Status Public on Jan 07, 2019
Title T+WSD11 (RNA-seq)
Sample type SRA
 
Source name white adipose tissue
Organism Macaca mulatta
Characteristics condition: testosterone + western style diet
Sex: female
age: 4 years old
tissue: white adipose tissue
Treatment protocol Visceral (omental) adipose tissue biopsies were collected in year 3 of treatment.
Growth protocol Young adult female rhesus macaques received testosterone (to mimic hyperandrogenemia) or control cholesterol implants for 3 years. Animals were maintained either on monkey chow (control) or high-fat western-style diet.
Extracted molecule total RNA
Extraction protocol RNA extracted using the AllPrep DNA/RNA purification kit (QIAGEN) according to the manufacturer’s instructions
High-quality RNA samples (RIN >8) were used for library construction using the TruSeq Rybo-zero method
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description ECP7.RNAseq.processed.rawCounts.txt
Data processing base calling
Sequencing reads were evaluated with FastQC (v0.11.5)
adapters and low quality bases trimmed with Trimmomatic (v0.36)
trimmed reads aligned to Mmul8 reference genome with STAR (v2.5.2b) with default parameters
Gene counts were obtained via STAR with the “--quantMode GeneCounts” parameter and Ensembl annotation (Mmul8 version 92)
DESeq2 (v1.18.1) used for differential gene expression analysis
Genome_build: Mmul8
Supplementary_files_format_and_content: tab delimited text file containing the raw counts for each gene (Ensembl Gene ID) in each sample
 
Submission date Jan 06, 2019
Last update date Jan 08, 2019
Contact name Brett Davis
E-mail(s) davibr@ohsu.edu
Organization name Oregon Health and Science University
Street address 3181 SW Sam Jackson Park Rd
City Portland
State/province Oregon
ZIP/Postal code 97239
Country USA
 
Platform ID GPL21120
Series (2)
GSE124707 Hyperandrogenemia and western-style diet act synergistically on transcription and DNA methylation in visceral adipose tissue of a non-human primate model [RNA-Seq]
GSE124709 Hyperandrogenemia and western-style diet act synergistically on transcription and DNA methylation in visceral adipose tissue of a non-human primate model
Relations
BioSample SAMN10698014
SRA SRX5210285

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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