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Sample GSM684870 Query DataSets for GSM684870
Status Public on Feb 28, 2014
Title Tumor_18w_vechicle_DEN_134
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 95.28147516
ILMN_1358051 86.90177766
ILMN_1361746 112.1131272
ILMN_1351370 116.1658667
ILMN_1357910 344.2774047
ILMN_1352975 1854.466314
ILMN_1368384 127.6243469
ILMN_1355285 94.31862271
ILMN_1376898 148.1575351
ILMN_1368325 139.650783
ILMN_1353563 107.9830879
ILMN_1348794 298.6553912
ILMN_1364273 94.55253742
ILMN_1369433 610.3304425
ILMN_1349007 146.3510945
ILMN_1374156 101.1110396
ILMN_1360232 90.56179461
ILMN_1355155 719.8624821
ILMN_1362563 100.5707153
ILMN_1355815 98.71855104

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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