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Sample GSM710572 Query DataSets for GSM710572
Status Public on Feb 17, 2012
Title PDCCE_FreshFrozen_CRC010
Sample type RNA
Source name mouse derived colorectal explant tumor, colon primary, liver metastasis, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: Colon
metastatic tumor site: Liver
Treatment protocol PDCCE samples were treated with saline by intraperitoneal injection for 2.5 weeks.
Growth protocol Colorectal cancer cells extracted from previously generated explants were injected subcutaneously into the flanks of JAX NOD.CB17-PrkdcSCID-J mice (four-week-old female) and measured every 2-3 days with a vernier caliper until the volume of the tumor (V = L×2W×0.52 (L = longest diameter, W = shortest diameter)) reached approximately 500 mm³. Tumors were grown for three additional weeks then were harvested and flash frozen.
Extracted molecule total RNA
Extraction protocol Frozen PDCCE samples were sectioned at 8µm and placed onto histological slides. An initial section was stained with hematoxylin and eosin (Sigma) for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 µg of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, CA). RNA were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE), and quality was assessed by spectrophotomeric analysis on an Agilent 2100 Bioanalyzer conductor using the RNA 6000 nano assay Kit (Agilent Technologies, Santa Clara, CA).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
Scan protocol GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
Data processing The gene expression data were RMA-estimated using the R statistical platform with the Bioconductor affymetrix package.
Submission date Apr 18, 2011
Last update date May 14, 2012
Contact name David Hsu
Phone 919-684-1739
Fax 919-668-4777
Organization name Duke University
Department Institute for Genome Sciences and Policy
Street address Rm 2167 CIEMAS Bldg, 101 Science Dr.
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
Platform ID GPL571
Series (1)
GSE28691 Characterization of an Oxaliplatin Sensitivity Predictor in a preclinical Murine Model of Colorectal Cancer

Data table header descriptions
VALUE Log2 GC-RMA signal

Data table
1007_s_at 10.05073586
1053_at 8.259846377
117_at 4.676655168
121_at 8.035499111
1255_g_at 3.601997472
1294_at 6.247344245
1316_at 5.217254653
1320_at 5.205374533
1405_i_at 4.221524602
1431_at 3.316080912
1438_at 7.180340625
1487_at 8.330352798
1494_f_at 5.012647046
1598_g_at 8.661664511
160020_at 6.398223302
1729_at 7.320535353
1773_at 5.73725452
177_at 5.763247445
179_at 8.150668099
1861_at 6.204425944

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM710572.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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