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Sample GSM457707 Query DataSets for GSM457707
Status Public on May 15, 2010
Title SH17 Chinese prostate cancer
Sample type genomic
 
Source name Chinese prostate cancer
Organism Homo sapiens
Characteristics tissue: Prostate cancer
Extracted molecule genomic DNA
Extraction protocol Fresh frozen samples were digested by Proteinase K and RNaseA. DNA was extracted from these samples using phenol/chroloform.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.
Description Hybridized to human SNP 6.0 array
Data processing CEL files and CHP files generated by Affymetrix Genechip Operating Software. Very weakly hybridized SNPs were filtered by the same software. The signal intensity data from SNP array were analyzed by in-house software- GOLF and commerical software-Partek.
 
Submission date Sep 29, 2009
Last update date Mar 05, 2010
Contact name Xueying Mao
E-mail(s) x.mao@qmul.ac.uk
Organization name Queen Mary
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL6801
Series (1)
GSE18333 Distinct genomic differences in prostate cancer between Western countries and China

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AA 0.002591 AA 3505.264648 857.407104
SNP_A-1967418 BB 0.002281 BB 332.533264 905.612915
SNP_A-1969580 BB 0.004760 BB 2000.655640 4393.952148
SNP_A-4263484 AB 0.007765 AB 1642.527588 1168.911133
SNP_A-1978185 AA 0.002302 AA 1169.393799 346.003967
SNP_A-4264431 AB 0.007508 AB 1607.639893 997.299622
SNP_A-1980898 BB 0.003743 BB 238.385330 1054.648071
SNP_A-1983139 AA 0.000735 AA 2730.141846 917.552307
SNP_A-4265735 AA 0.004111 AA 1792.553711 572.621277
SNP_A-1995832 AB 0.004264 AB 1873.551147 1826.297607
SNP_A-1995893 AB 0.001340 AB 2007.632202 2214.844238
SNP_A-1997689 BB 0.007754 BB 833.673462 2348.933350
SNP_A-1997709 AA 0.003052 AA 1338.166504 288.325623
SNP_A-1997896 AA 0.007239 AA 2102.193604 628.855530
SNP_A-1997922 AB 0.002598 AB 729.744690 618.589600
SNP_A-2000230 AA 0.003296 AA 2052.489746 1024.557983
SNP_A-2000332 AA 0.004528 AA 3470.448975 782.085022
SNP_A-2000337 AA 0.001465 AA 1636.368042 310.162109
SNP_A-2000342 AA 0.002768 AA 3024.554199 1071.325806
SNP_A-4268173 AA 0.003700 AA 1904.803467 496.580505

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM457707_SH17_T_GenomeWideSNP_6_.CEL.gz 27.4 Mb (ftp)(http) CEL
GSM457707_SH17_T_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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