|
| Status |
Public on Mar 24, 2020 |
| Title |
vWAT, 1 week, high fat diet, rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
visceral (epididymal) adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 7 weeks
Sex: male
diet: High fat diet (D12492)
time: 1 week
tissue: visceral (epididymal) adipose tissue
|
| Treatment protocol |
All mice were fed with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age a total of 170 and 180 mice were put on HFD (D12492, Research Diet) and chow diet (D12450J, Research Diet, respectively. Mice were sacrified after 1, 8 or 20 week of diet.
|
| Growth protocol |
C57/BL6 male, 4-wk-old (at time of sacrifice), mice were housed in a 12 h light/12 h dark (LD) regimen with water and food available ad libitum. All mice were fed with a 10% in fat chow diet (D12450J, Research Diet) for two weeks. At 6 weeks of age they were either shifted to a high fat diet containing 60% in fat (D12492, Research Diet) or kept in control diet for 1, 8 and 20 weeks. At each time time point, 20 mice were sacrified using CO2. Subcutaneous and viceral adipose tissue were immediately collected, snap-frozen in liquid nitrogen and kept at −80°C for RNA extraction and chromatin preparation. For chromatin preparation, aliquats of 4 grams of adipose tissue were homogenized on dry ice and immediately crosslinked in 45ml of PBS containing 0.5% formaldehyde. All animal care and handling was performed according to the Swiss law for animal protection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA, followed by purification with Lipid RNeasy Mini Kit (Qiagen). After quality check, total RNA from 4-10 individual mice of the same experimental group were pooled for RNA-seq.
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
1V_H1.3
|
| Data processing |
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8)
Reads were filtered for low complexity with reaper (v. 15-065)
Reads were aligned against Mus musculus.GRCm38.86 genome using STAR (v. 2.5.2b)
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) using Mus musculus.GRCm38.86 gene annotation.
Genome_build: Mus musculus.GRCm38.86
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read counts
|
| |
|
| Submission date |
Jun 13, 2019 |
| Last update date |
Mar 24, 2020 |
| Contact name |
Richard Coward |
| Organization name |
Bristol Royal hospital for Sick Children & University of Bristol
|
| Department |
Bristol Medical School
|
| Street address |
Dorothy Hodgkin Building, Whitson Street, Bristol
|
| City |
Lausanne |
| ZIP/Postal code |
BS1 3NY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE132706 |
Systemic approaches reveal anti-adipogenic signals at the onset of obesity–related inflammation in white adipose tissue [RNA-seq] |
| GSE132885 |
Systemic approaches reveal anti-adipogenic signals at the onset of obesity–related inflammation in white adipose tissue |
|
| Relations |
| BioSample |
SAMN12052628 |
| SRA |
SRX6068127 |
