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Sample GSM471608 Query DataSets for GSM471608
Status Public on Feb 28, 2014
Title wk18_DEN50_Erlotinib2_DEN_27
Sample type RNA
Source name rat liver, cirrhosis (DEN 50mg), treated with erlotinib 2mg (week 18)
Organism Rattus norvegicus
Characteristics strain: Wistar
sex: male
tissue: liver
disease status: cirrhosis
treatment group: treated with erlotinib 2mg
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_Erlotinib2_DEN_27
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 143.8101539
ILMN_1358051 122.967093
ILMN_1361746 145.0222084
ILMN_1351370 166.5924876
ILMN_1357910 732.1121228
ILMN_1352975 527.627399
ILMN_1368384 146.0451717
ILMN_1355285 154.2623033
ILMN_1376898 207.5950487
ILMN_1368325 172.2130926
ILMN_1353563 153.177377
ILMN_1348794 2840.756004
ILMN_1364273 149.7478063
ILMN_1369433 2047.617971
ILMN_1349007 286.7875721
ILMN_1374156 139.1774691
ILMN_1360232 157.6151084
ILMN_1355155 2056.426325
ILMN_1362563 130.1892314
ILMN_1355815 139.1774691

Total number of rows: 22523

Table truncated, full table size 546 Kbytes.

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

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