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Sample GSM471601 Query DataSets for GSM471601
Status Public on Feb 28, 2014
Title wk18_PBS_None_PBS_18
Sample type RNA
 
Source name rat liver, control (PBS, week 18)
Organism Rattus norvegicus
Characteristics strain: Wistar
sex: male
tissue: liver
disease status: control
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_PBS_None_PBS_18
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 138.2046635
ILMN_1358051 139.6486997
ILMN_1361746 130.9734632
ILMN_1351370 176.2761301
ILMN_1357910 1159.013521
ILMN_1352975 157.8715271
ILMN_1368384 120.7922012
ILMN_1355285 127.6566147
ILMN_1376898 223.4164401
ILMN_1368325 172.0261314
ILMN_1353563 214.7699471
ILMN_1348794 2452.927972
ILMN_1364273 132.0449912
ILMN_1369433 3799.23387
ILMN_1349007 414.9655285
ILMN_1374156 127.6566147
ILMN_1360232 119.7878819
ILMN_1355155 2311.286685
ILMN_1362563 130.005461
ILMN_1355815 138.2046635

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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