|
| Status |
Public on Sep 22, 2023 |
| Title |
S4: HFD PCN 11 |
| Sample type |
SRA |
| |
|
| Source name |
duodenum
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
tissue: duodenum
diet: High-fat diet (HFD)
treatment: intraperitoneal 50 mg/kg PCN for four days once a day
|
| 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 |
Dec 17, 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) |
| GSE163407 |
Transcriptomic effect of high-fat diet and PCN treatment on the duodenum of C57BL/6N mice. |
|
| Relations |
| BioSample |
SAMN17103462 |
| SRA |
SRX9697621 |
