|
| Status |
Public on Aug 18, 2014 |
| Title |
DMN_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
liver tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
background strain: Wistar Hanover (Crl:WI[Gl/BRL/Han]IGS BR)
gender: male
tissue: liver
treatment_agent: Dimethylnitrosamine
treatment_name: Treatment
treatment_type: gastric gavage
treatment_duration: 7 days
treatment_dose [mg/kg/d]: 4
control_group: 3
|
| Treatment protocol |
Animals (8–10 weeks old) were assigned to dose groups (five rats/group) by weight using a weight stratification-based computer program. Substances were administered by gastric gavage for up to 14 days (in a volume of 5 ml/kg body weight/day) based on the group mean weekly body weight for each dose group.
|
| Growth protocol |
Male Wistar Hanover rats (Crl:WI[Gl/BRL/Han]IGS BR) from Charles River Laboratories, Inc. (Raleigh, NC) were maintained on certified rodent chow (Certified Rodent Diet 5200; Purina Mills, St. Louis, MO) ad libitum in individual suspended stainless steel wire-mesh cages. The animals were kept under controlled temperature (18–26°C), humidity (30–70%), and lighting (12 h light/dark cycle) and were acclimated for a minimum of 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA including miRNA was isolated using the miRNeasy Mini Kit (QIAGEN, Hilden, Germany). RNA integrity was checked with an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Pico Kit (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
pCp-Cy3
|
| Label protocol |
25ng total RNA was end-labeled using the miRNA complete labeling and hybridization kit (Agilent# 5190-0456).
|
| |
|
| Hybridization protocol |
Arrays were hybridized according to the Agilent miRNA microarray method ‘miRNA Microarray System with miRNA Complete Labeling and Hyb Kit’ (G4170-90011).
|
| Scan protocol |
Following hybridization and washing, the arrays were scanned on an Agilent Microarray Scanner (#G2505B) according to the manufacturer’s protocol. Images from the scanner were processed using Agilent Feature Extraction Software v9.5.1.
|
| Data processing |
The raw microarray data was normalized using the Robust Multi-chip Average (RMA) method without background correction implemented in the package AgiMicroRna for R/Bioconductor. The probesets which were not expressed in any of the analyzed experimental conditions were removed.
|
| |
|
| Submission date |
Dec 06, 2013 |
| Last update date |
Aug 18, 2014 |
| Contact name |
Jonathan Moggs |
| E-mail(s) |
[email protected]
|
| Organization name |
Novartis
|
| Street address |
Fabrikstrasse 2
|
| City |
Basel |
| ZIP/Postal code |
4056 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL14889 |
| Series (3) |
| GSE53083 |
Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat (miRNA) |
| GSE53085 |
Cross-platform toxicogenomics for the prediction of nongenotoxic hepatocarcinogenesis in rat |
| GSE68387 |
IMI MARCAR Project: towards novel biomarkers for cancer risk assessment |
|
