|
| Status |
Public on Feb 05, 2024 |
| Title |
iWAT-KO-HFD-1 |
| Sample type |
SRA |
| |
|
| Source name |
iWAT
|
| Organism |
Mus musculus |
| Characteristics |
tissue: iWAT
strain: C57BL/6N
genotype: Acod1-/-
treatment: high fat diet
time: 16 weeks
Sex: male
|
| Treatment protocol |
C57BL/6NJ male wild type and Acod1-/- mice were challenged with HFD. HFD was started at 5 weeks of age and continued for 16 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from iWAT and eWAT was harvested from snap-frozen tissues using TRIZOL followed by the ReliaPrep RNA Tissue Miniprep System (Promega Cat#Z6111)
Barcoded mRNA Libraries were prepared usingNEBNext RNA Ultra II Directional Library Kit (New England Biolabs)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The 3' adaptors were removed using cutadapt and trimmed reads with a length of less than 18bp were discarded
The trimmed reads were filtered with a contaminants database consisting of rDNA sequences
The recovered non matching reads were aligned to the genome/transcriptome using STAR-align
Unique mappers from the resulting BAM file were used to create unstranded, stranded and reverse stranded coverage tracks for visualisation using bedtools
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample
|
| |
|
| Submission date |
Sep 19, 2022 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Tanja Eberhart |
| Organization name |
IRCCS San Raffaele Scientific Institute
|
| Street address |
Via Olgettina
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE213632 |
Transcriptomic signature of white adipose tissue from wild type and Acod1-deficient mice in response to high fat diet |
|
| Relations |
| BioSample |
SAMN30921253 |
| SRA |
SRX17625047 |
