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Sample GSM471596 Query DataSets for GSM471596
Status Public on Feb 28, 2014
Title wk12_DEN100__DEN_111
Sample type RNA
 
Source name rat liver, cirrhosis (DEN 100mg, 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_DEN100__DEN_111
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 128.3567338
ILMN_1358051 130.162886
ILMN_1361746 265.9227569
ILMN_1351370 136.8960117
ILMN_1357910 652.2041382
ILMN_1352975 1082.254067
ILMN_1368384 304.5317147
ILMN_1355285 138.1026428
ILMN_1376898 183.6813531
ILMN_1368325 170.3250958
ILMN_1353563 174.2583841
ILMN_1348794 752.8684706
ILMN_1364273 157.0428409
ILMN_1369433 687.0208668
ILMN_1349007 327.9979077
ILMN_1374156 127.5821372
ILMN_1360232 197.6255297
ILMN_1355155 991.5776897
ILMN_1362563 127.5821372
ILMN_1355815 151.1974496

Total number of rows: 22523

Table truncated, full table size 545 Kbytes.




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

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