|
| Status |
Public on Feb 10, 2014 |
| Title |
liver-tumor-ctnnb1-rep4 |
| Sample type |
RNA |
| |
|
| Source name |
Ctnn1b-mutated liver tumor tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H/HeJ
tissue: liver
treatment_agent: Phenobarbital
treatment_name: Phenobarbital
treatment_type: diet
treatment_route: oral
treatment_frequency: ad libitum
treatment_duration: 27 weeks
|
| Treatment protocol |
Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28).
|
| Growth protocol |
29–32 days old male C3H/HeJ mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10).
|
| 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 AFE-TGS method implemented in the package AgiMicroRna for R (v.2.14.1)/Bioconductor (v.2.9). Quantile normalization was applied to correct for experimental variation between arrays. The normalized total gene signals (TGS) were log2-transformed and probesets which were not expressed in any of the analyzed experimental conditions were removed.
|
| |
|
| Submission date |
Oct 17, 2013 |
| Last update date |
Feb 11, 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 |
GPL8824 |
| Series (3) |
| GSE51356 |
Metabolic programs orchestrated by the activated Ha-ras and Îroteins in mouse liver tumors [miRNA] |
| GSE51358 |
Metabolic programs orchestrated by the activated Ha-ras and β-catenin oncoproteins in mouse liver tumors |
| GSE68387 |
IMI MARCAR Project: towards novel biomarkers for cancer risk assessment |
|
