|
Status |
Public on Sep 22, 2023 |
Title |
Liver HFD PCN 688 |
Sample type |
SRA |
|
|
Source name |
liver
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6N genotype: PXR deficient diet: High-fat diet (HFD) treatment: intraperitoneal 50 mg/kg PCN for four days once a day tissue: Liver
|
Treatment protocol |
Obese mice were treated with PCN (50 mg/kg intraperitoneally) or vehicle for four days once a day.
|
Growth protocol |
6-week old mice were kept on regular chow or high-fat diet for 18-weeks to induce obesity and obesity-related metabolic impairments.
|
Extracted molecule |
total RNA |
Extraction protocol |
Liver pieces were lysed to RNAzol RT (Sigma-Aldrich) and total RNA was extracted per manufacturer's protocol. Samples were DNAse treated with Rnase-free Dnase set (Qiagen) cDNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
NextSeq 550 |
|
|
Data processing |
Base calling was done with Real-Time Analysis (RTA) software version 2. 75 base pair paired-end reads were aligned to mouse Ensembl reference genome GRCm38.95 with HISAT2 Reads per gene were counted with HTSeq Differentially expressed genes were determined with DESeq2 using Benjamini-Hochberg corrected adjusted p-value cutoff of <0.05 Genome_build: mm10 Supplementary_files_format_and_content: .txt files which include differentially expressed genes, reads per gene in all samples and log2 fold changes.
|
|
|
Submission date |
Nov 26, 2020 |
Last update date |
Sep 22, 2023 |
Contact name |
Jukka Hakkola |
E-mail(s) |
jukka.hakkola@oulu.fi
|
Organization name |
University of Oulu
|
Department |
Research Unit of Biomedicine
|
Street address |
Aapistie 5
|
City |
Oulu |
ZIP/Postal code |
90220 |
Country |
Finland |
|
|
Platform ID |
GPL21626 |
Series (1) |
GSE162196 |
Transcriptomic effect of high-fat diet and PCN treatment on the livers of of PXR deficient mice |
|
Relations |
BioSample |
SAMN16926499 |
SRA |
SRX9590323 |