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Sample GSM1019522 Query DataSets for GSM1019522
Status Public on Dec 31, 2016
Title HumanTumor_FreshFrozen_PRI_DH128
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 3
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 12.20455906
1053_at 7.822541139
117_at 8.225087012
121_at 9.721696181
1255_g_at 4.539020957
1294_at 8.477044595
1316_at 6.859791549
1320_at 6.321839553
1405_i_at 9.195444163
1431_at 5.405940921
1438_at 10.6176792
1487_at 10.37628072
1494_f_at 7.306063687
1552256_a_at 9.908375857
1552257_a_at 10.00920038
1552258_at 7.405241249
1552261_at 7.555948537
1552263_at 7.755022773
1552264_a_at 8.461268639
1552266_at 6.091685404

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1019522_PRI_DH128.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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