|
| Status |
Public on Aug 02, 2022 |
| Title |
PBS_46 |
| Sample type |
SRA |
| |
|
| Source name |
PBS_46
|
| Organism |
Rattus norvegicus |
| Characteristics |
disease status: PBS-treated healthy control
drug treatment: No treatment
|
| Treatment protocol |
8-week old male Wistar rats received weekly intraperitoneal injections of 50 mg/kg DEN to induce cirrhosis and HCC, or PBS, once per week over the course of 18 weeks. After 8 weeks, DEN-injured rats were randomly assigned to receive vehicle control (0.5% methylcelluose) or 20 mg/kg captopril by oral gavage daily for 9 weeks. Livers were harvested and analyzed in week 18.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini kit (QIAGEN) in accordance with manufacturer’s instructions.
High-quality total RNA samples (RNA Integrity score > 8 by Agilent Bioanalyzer) were subjected to poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol. The libraries were sequenced by NextSeq 550 genome sequencer (Illumina) to generate 100 bp single-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
PBS-treated control rats
|
| Data processing |
Raw reads were aligned to the reference genome (Rattus norvegicus, Rnor_6.0) using the spliced gap aligner STAR, and count-based quantitation was carried out by the Subread package featureCounts at the gene level based on ENSEMBL annotation build (Rnor_6.0.101). The whole-genome transcriptome read count data were normalized and modeled as over-dispersed Poisson data as TMM using a negative binomial model in the Bioconductor package edgeR. For subsequent data analysis, genes with no expression in more than 50% of the samples and low variance across the samples (coefficient of variance < 0.01) were excluded. The rat genes were mapped onto human orthologues based on NCBI Homologene database (build 68), and expression levels of multiple rat genes mapped to a human gene were summarized with their median value.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: gct format; the normalized read count mapped to rat genes and converted to human genes
|
| |
|
| Submission date |
Sep 14, 2020 |
| Last update date |
Aug 02, 2022 |
| Contact name |
Shijia Zhu |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota Medical School
|
| Department |
Department of Laboratory Medicine and Pathology
|
| Street address |
1200 Washington Avenue S Suite #175
|
| City |
Minneapolis |
| State/province |
Minnesota |
| ZIP/Postal code |
55415 |
| Country |
USA |
| |
|
| Platform ID |
GPL25029 |
| Series (1) |
| GSE157919 |
Captopril treatment in rats with DEN-induced cirrhosis and hepatocellular carcinoma |
|
| Relations |
| BioSample |
SAMN16129602 |
