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Sample GSM471599 Query DataSets for GSM471599
Status Public on Feb 28, 2014
Title wk18_PBS_None_PBS_8
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_8
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 160.6519592
ILMN_1358051 131.9818167
ILMN_1361746 125.8998832
ILMN_1351370 140.1603138
ILMN_1357910 785.1489034
ILMN_1352975 244.7649147
ILMN_1368384 128.900911
ILMN_1355285 143.9930508
ILMN_1376898 211.2920739
ILMN_1368325 168.2433444
ILMN_1353563 203.458579
ILMN_1348794 1949.249797
ILMN_1364273 146.4472217
ILMN_1369433 3335.848776
ILMN_1349007 350.7488432
ILMN_1374156 171.7307477
ILMN_1360232 128.1854114
ILMN_1355155 2283.201477
ILMN_1362563 129.6078419
ILMN_1355815 133.9027763

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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