|
| Status |
Public on Apr 27, 2022 |
| Title |
Brown adipose tissue, cBATKO_TH_10 |
| Sample type |
SRA |
| |
|
| Source name |
Brown adipose tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brown adipose tissue
age: 8-12 weeks
Sex: Male
background strain: C57BL/6J
genotype: BATKO
treatment: PTU+TH 24h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted using Trizol. Total RNA was converted to cDNA using MMLV reverse transcriptase. 1ug of total RNA was used for the construction of sequencing libraries
cDNA libraries were prepared using the total RNA SENSE kit (Lexogen, Vienna, Austria) and analyzed on a Nextseq 500 sequencer (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
TH kinetics.txt
BATKO_TH_10
|
| Data processing |
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.3.2.2 with default parameters
Read were counted using htseqcount Galaxy version 0.6.1galaxy3 using these parameters // Mode : Union / Stranded : Reverse / Minimul alignement quality : 10 / Feature type : exon / ID Attribute : gene name
Differential gene expression analysis was performed with DESeq2 (R package, Version 1.34.0) using the following thresholds: adjusted p-value <0.05; average expression > 10 reads per million, log2 fold-change > 0.6 or < -0.6. The effect of mutations on both cold exposure and HFD was obtained using the interaction model (Ge, 2021). Thresholds for the interaction were the following: average expression > 10 reads per million, adjusted p-value < 0.05.
Differentially expressed genes expression was visualized as clustered heatmaps using Pheatmap R package (RRID:SCR_016418)
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts of all samples from the same experiment (TH injection for target genes, cold exposure and HFD in 3 different tables. Each sample is preceded by a, b or c, which allows to quickly identify the 3 different experiments)
|
| |
|
| Submission date |
Apr 20, 2022 |
| Last update date |
Apr 27, 2022 |
| Contact name |
Yanis ZEKRI |
| E-mail(s) |
[email protected]
|
| Organization name |
IGFL-ENS
|
| Street address |
32-34 Avenue Tony Garnier
|
| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE201135 |
Target genes of thyroid hormone (TH) in brown adipose tissue (BAT) and their role during metabolic stressors [RNA-seq] |
| GSE201136 |
Target genes of thyroid hormone (TH) in brown adipose tissue (BAT) and their role during metabolic stressors |
|
| Relations |
| BioSample |
SAMN27671360 |
| SRA |
SRX14935305 |
