|
| Status |
Public on Jun 30, 2023 |
| Title |
Hamster HFD-T070 5% 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mesocricetus auratus |
| Characteristics |
tissue: Liver
genotype: WT
treatment: High Fat Diet + Totum-070 5%
|
| Treatment protocol |
Hamster were fed with either a Normal Diet, a High Fat Diet or a High Fat Diet mixed with Totum-070 mixed in the diet at 5% for 6 complet weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from snap-frozen tissues using TRIzol.
Fragmented double-strand cDNA was synthesized using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
66_C
|
| Data processing |
FASTQ files were generated using bcl2fastq (Illumina).
Reads were trimmed with Trimmomatic (version 0.36) to filter poor quality reads and to cut adapters. Filtered reads were mapped to the reference genome (Mesocricetus auratus, assembly MesAur1) using STAR (version 2.7.10). The STAR software was also used to produce the count matrix to assign reads to features using transcriptome annotations from the GTF file.
The differential analysis was performed with the edgeR R package. TMM normalization was applied. The glmQLFit and glmQLFTest functions were used to identify differentially expressed genes in the three groups (ND, HFD and HFD-T070 5%).
Assembly: Mesocricetus auratus, assembly MesAur1
Supplementary files format and content: A single tab-delimited text file including raw counts for each sample as a column
|
| |
|
| Submission date |
Mar 15, 2023 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Cédric Langhi |
| E-mail(s) |
cedric.langhi@valbiotis.com
|
| Organization name |
Valbiotis
|
| Street address |
20-22 rue Henri et Gilberte Goudier
|
| City |
Riom |
| ZIP/Postal code |
63200 |
| Country |
France |
| |
|
| Platform ID |
GPL24490 |
| Series (1) |
| GSE227411 |
Totum-070, a nutritional combination of plant extracts, prevents hypercholesterolemia in high fat diet-fed hamsters by inhibiting intestinal cholesterol absorption |
|
| Relations |
| BioSample |
SAMN33770344 |
| SRA |
SRX19682091 |
