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Sample GSM457742 Query DataSets for GSM457742
Status Public on May 15, 2010
Title SH36 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 Apr 18, 2011
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 0.009314 AA 4093.091797 1316.699341
SNP_A-1967418 NC 0.109479 AB 806.379333 523.729248
SNP_A-1969580 BB 0.017402 BB 2154.515137 4193.194336
SNP_A-4263484 AB 0.013899 AB 1736.640869 1663.412720
SNP_A-1978185 AB 0.003577 AB 921.743652 844.149719
SNP_A-4264431 AB 0.002353 AB 1389.988037 1081.083862
SNP_A-1980898 BB 0.004183 BB 267.546387 992.395813
SNP_A-1983139 AA 0.008813 AA 3325.742188 1089.341064
SNP_A-4265735 BB 0.013370 BB 984.927185 2603.929688
SNP_A-1995832 BB 0.000137 BB 845.591370 2668.428467
SNP_A-1995893 BB 0.004340 BB 597.140625 2968.367432
SNP_A-1997689 BB 0.014305 BB 779.488098 1945.924805
SNP_A-1997709 AA 0.002134 AA 1261.196411 284.634430
SNP_A-1997896 AA 0.006725 AA 1408.528320 686.065735
SNP_A-1997922 BB 0.009356 BB 459.071014 781.024597
SNP_A-2000230 AA 0.011162 AA 1538.612305 871.871887
SNP_A-2000332 AB 0.010272 AB 2641.923340 2851.015869
SNP_A-2000337 AA 0.015050 AA 2052.801514 347.537476
SNP_A-2000342 AA 0.004927 AA 2825.745117 1206.046143
SNP_A-4268173 AA 0.005383 AA 1229.295288 353.015228

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.




Supplementary file Size Download File type/resource
GSM457742_SH36_T_GenomeWideSNP_6_.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM457742_SH36_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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