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Sample GSM471593 Query DataSets for GSM471593
Status Public on Feb 28, 2014
Title wk12_DEN50__DEN_11
Sample type RNA
 
Source name rat liver, cirrhosis (DEN 50mg, week 12)
Organism Rattus norvegicus
Characteristics strain: Wistar
sex: male
tissue: liver
disease status: cirrhosis
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 wk12_DEN50__DEN_11
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 130.9839653
ILMN_1358051 130.9839653
ILMN_1361746 185.7069555
ILMN_1351370 153.8786543
ILMN_1357910 360.5593305
ILMN_1352975 211.5120724
ILMN_1368384 176.6450507
ILMN_1355285 138.8778885
ILMN_1376898 195.8588902
ILMN_1368325 189.8357594
ILMN_1353563 179.8306999
ILMN_1348794 1948.787957
ILMN_1364273 178.2567207
ILMN_1369433 1714.47509
ILMN_1349007 382.7573839
ILMN_1374156 134.8524417
ILMN_1360232 171.6687345
ILMN_1355155 1648.943248
ILMN_1362563 130.9839653
ILMN_1355815 143.5617976

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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