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Sample GSM1019415 Query DataSets for GSM1019415
Status Public on Dec 31, 2016
Title HumanTumor_FreshFrozen_MET_CRC057A
Sample type RNA
 
Source name human tumor, colorectal primary, metastasis, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: colorectal
metastatic tumor site: Liver
molecular subgroup: MSCC 1
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 12.47819788
1053_at 8.682753357
117_at 8.423760831
121_at 9.763357506
1255_g_at 4.339044106
1294_at 9.006734784
1316_at 6.474648427
1320_at 6.12470837
1405_i_at 6.683624065
1431_at 9.454680918
1438_at 9.272456596
1487_at 9.636932957
1494_f_at 7.576402433
1552256_a_at 11.00909898
1552257_a_at 10.36542222
1552258_at 7.11238996
1552261_at 6.397632334
1552263_at 8.692004669
1552264_a_at 8.433753783
1552266_at 5.579693558

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1019415_MET_CRC057A.CEL.gz 5.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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