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Sample GSM471602 Query DataSets for GSM471602
Status Public on Feb 28, 2014
Title wk18_DEN50_Vehicle_DEN_24
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_24
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
E-mail(s) Yujin.Hoshida@UTSouthwestern.edu
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
ID_REF
VALUE cubic spline normalized signal intensity

Data table
ID_REF VALUE
ILMN_1369537 202.3014189
ILMN_1358051 119.2073143
ILMN_1361746 178.653316
ILMN_1351370 158.5833715
ILMN_1357910 642.600317
ILMN_1352975 673.1751395
ILMN_1368384 176.9639763
ILMN_1355285 124.2836228
ILMN_1376898 203.8945781
ILMN_1368325 143.9318823
ILMN_1353563 152.620641
ILMN_1348794 2196.432098
ILMN_1364273 166.0189601
ILMN_1369433 1419.134745
ILMN_1349007 286.8776955
ILMN_1374156 126.8799258
ILMN_1360232 295.4496355
ILMN_1355155 967.224264
ILMN_1362563 121.3200211
ILMN_1355815 145.4683184

Total number of rows: 22523

Table truncated, full table size 548 Kbytes.




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

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