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Sample GSM684866 Query DataSets for GSM684866
Status Public on Feb 28, 2014
Title Tumor_18w_erlotinib2_DEN_127
Sample type RNA
 
Source name rat, hepatocellular carcinoma (DEN 50mg), treated with erlotinib 2mg (week 18)
Organism Rattus norvegicus
Characteristics tissue: hepatocellular carcinoma tumor
treatment: erlotinib 2mg
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 105.9238639
ILMN_1358051 90.08160173
ILMN_1361746 92.98016219
ILMN_1351370 101.2822191
ILMN_1357910 157.7523514
ILMN_1352975 4692.566081
ILMN_1368384 239.7530343
ILMN_1355285 95.16273307
ILMN_1376898 101.2822191
ILMN_1368325 136.6079025
ILMN_1353563 124.051721
ILMN_1348794 95.25489547
ILMN_1364273 105.0983844
ILMN_1369433 645.7000525
ILMN_1349007 144.7554299
ILMN_1374156 90.94441093
ILMN_1360232 115.7505453
ILMN_1355155 447.2034558
ILMN_1362563 101.2822191
ILMN_1355815 97.21585574

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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