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Sample GSM1019406 Query DataSets for GSM1019406
Status Public on Dec 31, 2016
Title HumanTumor_FreshFrozen_MET_CRC043A
Sample type RNA
 
Source name human tumor, colorectal primary, metastasis, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: colorectal
metastatic tumor site: Lung
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 11.31796258
1053_at 7.768591493
117_at 7.985595365
121_at 9.661253243
1255_g_at 4.896029418
1294_at 8.581237251
1316_at 6.891593482
1320_at 6.366300237
1405_i_at 7.141819568
1431_at 6.010948392
1438_at 9.195450556
1487_at 8.894572154
1494_f_at 7.867554164
1552256_a_at 10.19237234
1552257_a_at 9.584555241
1552258_at 7.219849485
1552261_at 7.310882799
1552263_at 6.779122394
1552264_a_at 7.414695858
1552266_at 6.408961099

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1019406_MET_CRC043A.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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