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Sample GSM684868 Query DataSets for GSM684868
Status Public on Feb 28, 2014
Title Tumor_18w_vechicle_DEN_123
Sample type RNA
 
Source name rat, hepatocellular carcinoma (DEN 50mg), treated with vehicle (week 18)
Organism Rattus norvegicus
Characteristics tissue: hepatocellular carcinoma tumor
treatment: vehicle
strain: Wistar
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 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. 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 Standard Illumina protocol, refer to the Illumina beadarray Assay System Manual
 
Hybridization protocol Standard Illumina protocol, refer to the Illumina beadarray Assay System Manual
Scan protocol Standard Illumina protocol, refer to the Illumina beadarray Assay System Manual
Data processing For each probe, replicated mesurements (beads) were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm.
 
Submission date Mar 02, 2011
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)
GSE27638 Gene expression profile of hepatocellular carcinoma 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 intensities by GenePattern IlluminaNormalizer module

Data table
ID_REF VALUE
ILMN_1369537 106.1809271
ILMN_1358051 90.26350347
ILMN_1361746 92.40506986
ILMN_1351370 96.47610954
ILMN_1357910 150.1660945
ILMN_1352975 1227.130035
ILMN_1368384 245.9291246
ILMN_1355285 98.96555776
ILMN_1376898 104.5650244
ILMN_1368325 141.9037838
ILMN_1353563 146.360436
ILMN_1348794 141.2533875
ILMN_1364273 101.2255076
ILMN_1369433 163.7714849
ILMN_1349007 141.2533875
ILMN_1374156 90.86714792
ILMN_1360232 92.98586427
ILMN_1355155 374.5232265
ILMN_1362563 98.96555776
ILMN_1355815 96.47610954

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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