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Sample GSM1019509 Query DataSets for GSM1019509
Status Public on Dec 31, 2016
Title HumanTumor_FreshFrozen_PRI_DH057
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 11.10138592
1053_at 8.566998011
117_at 7.81226368
121_at 9.407271405
1255_g_at 4.573412566
1294_at 9.3423841
1316_at 6.80620291
1320_at 6.065852055
1405_i_at 8.465501712
1431_at 5.04098839
1438_at 11.03617408
1487_at 9.619804009
1494_f_at 7.163536756
1552256_a_at 10.79486997
1552257_a_at 10.22690571
1552258_at 7.099887647
1552261_at 6.388564999
1552263_at 7.959060816
1552264_a_at 8.137880322
1552266_at 5.862052631

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1019509_PRI_DH057.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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