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Sample GSM457683 Query DataSets for GSM457683
Status Public on May 15, 2010
Title SH3 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 BB 0.008485 BB 1463.491943 4326.952148
SNP_A-1967418 AB 0.002740 AB 791.007202 743.270630
SNP_A-1969580 BB 0.005191 BB 2007.740723 4802.242188
SNP_A-4263484 AA 0.005925 AA 2934.268066 690.627869
SNP_A-1978185 AB 0.025306 AB 1320.044434 1217.571289
SNP_A-4264431 BB 0.005983 BB 905.953613 1884.522461
SNP_A-1980898 BB 0.006174 BB 352.205231 1052.569092
SNP_A-1983139 AB 0.009082 AB 2116.604492 1744.289307
SNP_A-4265735 AB 0.002351 AB 1626.029541 1635.665039
SNP_A-1995832 BB 0.015699 BB 1243.709839 3382.140137
SNP_A-1995893 BB 0.031382 BB 1056.350708 3877.607422
SNP_A-1997689 BB 0.005887 BB 964.000183 2717.569580
SNP_A-1997709 AA 0.006509 AA 1619.932861 348.509644
SNP_A-1997896 AA 0.007996 AA 1300.557007 628.096863
SNP_A-1997922 BB 0.010818 BB 660.631165 934.495605
SNP_A-2000230 AA 0.001021 AA 1912.255737 1140.835205
SNP_A-2000332 AB 0.008433 AB 2229.722412 2174.210693
SNP_A-2000337 AA 0.006366 AA 1872.979858 321.633392
SNP_A-2000342 AA 0.018650 AA 3132.364258 1491.974976
SNP_A-4268173 AA 0.010785 AA 1011.580750 264.623840

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.




Supplementary file Size Download File type/resource
GSM457683_SH3_T_GenomeWideSNP_6_.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM457683_SH3_T_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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