|
| Status |
Public on Jan 07, 2019 |
| Title |
C3 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
white adipose tissue
|
| Organism |
Macaca mulatta |
| Characteristics |
condition: control
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) |
[email protected]
|
| 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 |
SAMN10697974 |
| SRA |
SRX5210276 |
