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Sample GSM902293 Query DataSets for GSM902293
Status Public on Mar 31, 2012
Title DEN_LT684T1
Sample type RNA
 
Source name DEN induced liver tumor (HCC), Trp53 wt
Organism Mus musculus
Characteristics tissue: HCC
strain: C57BL/6J
genotype: TTD-
Treatment protocol mice (group: DEN induced liver tumors) were treated at day 15 with DEN (i.p.; 10µg/g bodyweight)
Growth protocol mice were kept in a pathogen-free environment
Extracted molecule total RNA
Extraction protocol RNA was isolated using the RNzol following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer
 
Hybridization protocol 1.65 µg of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 55 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K V2 Microarrays (G4846A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (5micron) with the the Agilent Scan Control Version A.8.4.1 .
Description DEN treated
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). The data was preprocessed according to Agilent's Genespring software standard workflow. Gene expression levels were background corrected and signals for duplicated probes were summarized by geometric mean of non-compromised probes. After log2 transformation, a percentile shift normalization at the 75% level and a baseline shift to the median baseline of all probes was performed.
 
Submission date Mar 26, 2012
Last update date Apr 04, 2012
Contact name Hans A Kestler
E-mail(s) hans.kestler@uni-ulm.de
Phone +49 731 5024248
Organization name University of Ulm
Department Research Group Bioinformatics and Systems Biology
Street address Albert-Einstein-Allee 11
City Ulm
ZIP/Postal code 89081
Country Germany
 
Platform ID GPL11202
Series (1)
GSE36813 Transient telomere dysfunction induces chromosomal instability and promotes carcinogenesis in telomerase-proficient mice

Data table header descriptions
ID_REF
VALUE Normalized intensity values (log2)

Data table
ID_REF VALUE
GE_BrightCorner -0.223503845
DarkCorner -0.455627932
A_55_P1989846 -0.616418461
A_55_P1991598 -0.151836032
A_55_P2022211 0.392684042
A_55_P1980764 -0.114252523
A_55_P1964375 0.412109182
A_51_P128876 -0.798993641
A_55_P2121042 -0.154460407
A_52_P219230 -2.151612288
A_51_P207591 3.81604702
A_55_P2131920 0.619259596
A_55_P2404223 0.38763082
A_55_P2101944 -1.061712767
A_52_P358860 -0.020457431
A_51_P119031 -0.298838999
A_51_P309854 -4.617565203
A_51_P343900 -0.047392856
A_51_P234359 -0.006699766
A_51_P487813 0.027765897

Total number of rows: 39485

Table truncated, full table size 1004 Kbytes.




Supplementary file Size Download File type/resource
GSM902293_US81503234_252665512416_S01_GE1_107_Sep09_1_4.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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