|
| Status |
Public on Jun 10, 2021 |
| Title |
iWAT, KO_HFD_19 |
| Sample type |
SRA |
| |
|
| Source name |
iWAT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: female
tissue: subcutaneous inguinal white adipose tissue
diet: high fat diet
genotype: knock out
|
| Treatment protocol |
wild type vs knockout mice fed with high fat diet vs low fat diet
|
| Growth protocol |
6 months old, group caged, female mice fed with high fat vs low fat diet for 15 weeks. Ad libitum access to water. 12h dark and 12h light cyckles in air conditioned facility. Research Diets Inc. low fat diet(10.5% fat) - D12328; high fat diet(58% fat) - D12331
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated by Rneasy Lipid Tissue Kit (Qiagen) - cat. No. 74804
Illumina TruSeq Stranded Total RNA Gold kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Align to Mouse mm9 assembly with STAR v2.5.3.a
Filter for properly paired, unique alignments
Remove reads in blacklisted regions
Convert to bigWig
Pseudo-align reads with Salmon 0.13.1 and Ensembl 67 transcripts
Genome_build: mm9
Supplementary_files_format_and_content: bigWig coverage files per strand, TPM gene expresion file
|
| |
|
| Submission date |
Mar 16, 2020 |
| Last update date |
Jun 10, 2021 |
| Contact name |
Shaun Michael Webb |
| E-mail(s) |
shaun.webb@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
Wellcome Trust Centre for Cell Biology
|
| Lab |
Bioinformatics Core Facility
|
| Street address |
2.21 Swann Building, Kings Buildings
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE147016 |
RNA-seq analysis of subcutaneus inguinal adipose tissue from Tmem120a fat specific knockout mice (females) |
|
| Relations |
| BioSample |
SAMN14381466 |
| SRA |
SRX7917322 |
