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Sample GSM1243261 Query DataSets for GSM1243261
Status Public on Feb 10, 2014
Title liver-tumor-ctnnb1-rep7
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) jonathan.moggs@novartis.com
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

Data table header descriptions
ID_REF
VALUE log2-transformed quantile-normalized total gene signal

Data table
ID_REF VALUE
mghv-miR-M1-2 1.602915875
mmu-let-7a 10.89220312
mmu-let-7b 9.923961868
mmu-let-7c 9.974702903
mmu-let-7d 9.5240153
mmu-let-7d* -1
mmu-let-7e 5.812525821
mmu-let-7f 11.37011863
mmu-let-7g 9.699951946
mmu-let-7i 8.340891851
mmu-miR-100 -1
mmu-miR-101a 6.849309622
mmu-miR-101b 7.671434033
mmu-miR-103 7.168295853
mmu-miR-106b 6.076475321
mmu-miR-107 8.093964496
mmu-miR-10a 5.675029565
mmu-miR-122 13.33568684
mmu-miR-1224 9.351727422
mmu-miR-125a-5p 0.297653651

Total number of rows: 147

Table truncated, full table size 3 Kbytes.




Supplementary file Size Download File type/resource
GSM1243261_US10350382_251911911021_S01_miRNA_107_Sep09_2_4.txt.gz 668.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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