|
| Status |
Public on Jun 28, 2021 |
| Title |
DEN_1_255 |
| Sample type |
SRA |
| |
|
| Source name |
liver tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
Sex: male
disease status: cirrhosis (DEN-treated)
drug treatment: Vehicle
tissue: liver
|
| Treatment protocol |
8-week-old male Wistar rats received weekly intraperitoneal injections of low-dose (50 mg/kg) diethylnitrosamine (DEN) to induce liver cirrhosis and cancer or PBS as control. After 12 weeks, DEN-treated cirrhotic rats were randomly assigned to receive vehicle or 15 mg/kg nizatidine by oral gavage daily for 6 weeks. Livers were harvested and total RNA was isolated for transcriptome profiling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini kit (Qiagen), and cDNA was synthesized using the SuperScript III First-Strand Synthesis SuperMix Kit (Invitrogen) following manufacturer’s instructions.
Poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
lowdoseDENrat_NIZA.txt
|
| Data processing |
Adaptor sequences from raw sequencing reads were trimmed using trimmomatic (v0.36) prior to alignment. These reads were aligned to refence genome (rn4) using STAR 2-pass alignment procedure. Read counts were normalized for library size by Count Per Million (CPM) method, followed by trimmed mean of M-values (TMM) using edgeR R package. These normalized counts were log-transformed by log2(x+1). Genes with no expression in at least 50% of all samples or coefficient of variation (CV) less than 0.01 were filtered out.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited .txt file including normalized expression values (TMM) for each sample
|
| |
|
| Submission date |
Jun 07, 2018 |
| Last update date |
Jun 28, 2021 |
| Contact name |
Yujin Hoshida |
| E-mail(s) |
Yujin.Hoshida@UTSouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE66843 |
A cell-based model unravels drivers for hepatocarcinogenesis and targets for clinical chemoprevention |
| GSE115473 |
Transcriptome profiles of liver from cirrhotic rat treated with nizatidine |
|
| Relations |
| BioSample |
SAMN09379999 |
| SRA |
SRX4180232 |
