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Sample GSM471604 Query DataSets for GSM471604
Status Public on Feb 28, 2014
Title wk18_DEN50_Vehicle_DEN_69
Sample type RNA
Source name rat liver, cirrhosis (DEN 50mg), treated with vehicle (week 18)
Organism Rattus norvegicus
Characteristics strain: Wistar
sex: male
tissue: liver
disease status: cirrhosis
treatment group: treated with vehicle
Treatment protocol Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg, 100mg/kg, or vehicle control (PBS) for 18 weeks. A subset of rats received either daily (5X a week) IP injections of 2 mg/kg erlotinib or vehicle control during weeks 13 - 18. In a separate study, the erlotinib dose was lowered to 0.5 mg/kg. The vehicle groups from the two studies were not significantly different so they were combined together for analysis. Rats were weighed at the end of each week. Animals were sacrificed at 9, 13 and 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.
Extracted molecule total RNA
Extraction protocol Using frozen non-tumor liver tissues, total RNA was extracted using TRIzol (Invitrogen).
Label Cy5
Label protocol Refer to the Illumina beadarray Assay System Manual
Hybridization protocol Refer to the Illumina beadarray Assay System Manual
Scan protocol Refer to the Illumina beadarray Assay System Manual
Description wk18_DEN50_Vehicle_DEN_69
Data processing For each probe, replicate mesurements were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm using GenePattern IlluminaNormalizer module.
Submission date Nov 17, 2009
Last update date Feb 28, 2014
Contact name Yujin Hoshida
Organization name University of Texas Southwestern Medical Center
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
Platform ID GPL6101
Series (2)
GSE19057 Gene expression profile of liver tissue in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with erlotinib
GSE27641 EGFR inhibition prevents liver cirrhosis and hepatocellular carcinoma

Data table header descriptions
VALUE cubic spline normalized signal intensity

Data table
ILMN_1369537 163.8384413
ILMN_1358051 124.4552816
ILMN_1361746 203.028818
ILMN_1351370 144.3165081
ILMN_1357910 1300.677059
ILMN_1352975 908.6509524
ILMN_1368384 230.567267
ILMN_1355285 138.4480265
ILMN_1376898 206.1342373
ILMN_1368325 196.781885
ILMN_1353563 193.6721267
ILMN_1348794 1685.928363
ILMN_1364273 151.8492156
ILMN_1369433 862.9996505
ILMN_1349007 291.6183962
ILMN_1374156 135.7370836
ILMN_1360232 182.5652048
ILMN_1355155 1539.655117
ILMN_1362563 133.8517344
ILMN_1355815 137.5126661

Total number of rows: 22523

Table truncated, full table size 547 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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