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Sample GSM710565 Query DataSets for GSM710565
Status Public on Feb 17, 2012
Title HumanTumor_FreshFrozen_CRC059
Sample type RNA
 
Source name human tumor, colon primary, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: Colon
metastatic tumor site: Colon
Extracted molecule total RNA
Extraction protocol Tumors were flash frozen in OCT at time of surgical resection. An initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, 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
E-mail(s) hsu00018@dm.duke.edu
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
ID_REF
VALUE Log2 GC-RMA signal

Data table
ID_REF VALUE
1007_s_at 9.873158004
1053_at 6.651016367
117_at 10.85985899
121_at 7.623214235
1255_g_at 3.539592808
1294_at 7.25104734
1316_at 5.19159795
1320_at 5.08295367
1405_i_at 6.676921664
1431_at 3.758026358
1438_at 6.823893771
1487_at 7.837689653
1494_f_at 4.941691233
1598_g_at 8.389145183
160020_at 7.243114784
1729_at 7.762232394
177_at 6.169175013
1773_at 5.592109928
179_at 8.142487422
1861_at 6.04025061

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM710565.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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