|
| Status |
Public on May 12, 2021 |
| Title |
WT5-19 |
| Sample type |
SRA |
| |
|
| Source name |
Brown adipose tissue (supraclavicular)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
group: WT5
genotype: WT
temperature: 5
|
| Treatment protocol |
cold exposure for 6 hours
|
| Growth protocol |
Fat-specific Afadin KO and control littermates incubated at thermoneutrality for 2 weeks. Half were then transferred to cold (5 degrees celsius) for 6 hours. Mice were euthanized and BAT collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol/chloroform extraction
Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
1) RNAseq raw reads were aligned to mouse genome (mm10) using STAR v2.5.2b.
2) Gene read coverages were computed with featureCounts v1.5.2 using GENCODE annotation release M13
3) Differential expression analysis was performed using edgeR v3.22.0 with "y ~ 0 + group" design while filtering low count reads using built-in function filterByExpr
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of read counts
|
| |
|
| Submission date |
Mar 23, 2020 |
| Last update date |
May 12, 2021 |
| Contact name |
Ali Altintas |
| E-mail(s) |
[email protected]
|
| Organization name |
Copenhagen University
|
| Department |
NNF Center for Basic Metabolic Research
|
| Lab |
Integrative Physiology
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE147392 |
Cold-induction of Afadin in Brown Fat supports its thermogenic capacity |
|
| Relations |
| BioSample |
SAMN14426998 |
| SRA |
SRX7971193 |
