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Sample GSM1019518 Query DataSets for GSM1019518
Status Public on Dec 31, 2016
Title HumanTumor_FreshFrozen_PRI_DH114
Sample type RNA
 
Source name human tumor, colorectal primary, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: colorectal
metastatic tumor site: NA
molecular subgroup: MSCC 6
Extracted molecule total RNA
Extraction protocol Human 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 data were analyzed using the R statistical platform with the Bioconductor affymetrix package [R version 2.13.1 (2011-07-08) and Bioconductor version 2.9].
 
Submission date Oct 12, 2012
Last update date Dec 31, 2016
Contact name David Hsu
Organization name Duke University
Department Medical Oncology
Street address 905 S. LaSalle St. Rm 3008
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL570
Series (2)
GSE41568 A Molecular Profile of Colorectal Cancer to Guide Therapy [PDCCEs]
GSE51244 A Molecular Profile of Colorectal Cancer to Guide Therapy

Data table header descriptions
ID_REF
VALUE Log2 GC-RMA signal

Data table
ID_REF VALUE
1007_s_at 11.6002725
1053_at 7.821837117
117_at 7.717113275
121_at 9.870996346
1255_g_at 4.720473905
1294_at 8.795992229
1316_at 6.602197956
1320_at 6.210890321
1405_i_at 5.57829745
1431_at 5.311847141
1438_at 9.524424486
1487_at 9.743721778
1494_f_at 7.490920901
1552256_a_at 9.635210189
1552257_a_at 9.725065955
1552258_at 6.689027261
1552261_at 6.535530481
1552263_at 6.825792635
1552264_a_at 7.542088937
1552266_at 6.053492087

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1019518_PRI_DH114.CEL.gz 5.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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