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Sample GSM902295 Query DataSets for GSM902295
Status Public on Mar 31, 2012
Title DEN_LT697T3
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 (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
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
VALUE Normalized intensity values (log2)

Data table
GE_BrightCorner 0.150252749
DarkCorner -0.123132908
A_55_P1989846 -0.166323723
A_55_P1991598 -0.099331499
A_55_P2022211 -0.766912463
A_55_P1980764 0.359614212
A_55_P1964375 -0.158595401
A_51_P128876 0.163170737
A_55_P2121042 -0.091829283
A_52_P219230 0.096400171
A_51_P207591 -0.772527639
A_55_P2131920 -1.127896943
A_55_P2404223 0.010426949
A_55_P2101944 -0.000218461
A_52_P358860 0.294840376
A_51_P119031 -0.318674566
A_51_P309854 -0.308399823
A_51_P343900 -0.111161457
A_51_P234359 -0.205202601
A_51_P487813 -0.294839627

Total number of rows: 39485

Table truncated, full table size 1007 Kbytes.

Supplementary file Size Download File type/resource
GSM902295_US81503234_252665512417_S01_GE1_107_Sep09_1_2.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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