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Sample GSM457700 Query DataSets for GSM457700
Status Public on May 15, 2010
Title SH13 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 0.005225 AA 2778.662354 1017.101135
SNP_A-1967418 BB 0.003209 BB 449.919617 861.028870
SNP_A-1969580 BB 0.001446 BB 1677.237305 3618.755371
SNP_A-4263484 BB 0.004665 BB 697.697021 1762.196655
SNP_A-1978185 AB 0.003367 AB 919.417297 997.511902
SNP_A-4264431 AB 0.006710 AB 1476.895020 1149.420532
SNP_A-1980898 AB 0.003009 AB 836.915710 630.183472
SNP_A-1983139 AA 0.004304 AA 2191.081543 959.284607
SNP_A-4265735 AB 0.002105 AB 1289.922119 1334.835449
SNP_A-1995832 BB 0.008359 BB 792.607178 1735.264404
SNP_A-1995893 BB 0.004110 BB 623.805176 2255.165771
SNP_A-1997689 BB 0.009751 BB 923.438354 2100.509033
SNP_A-1997709 AA 0.004789 AA 1054.652710 239.142807
SNP_A-1997896 AA 0.001753 AA 1471.442993 771.771851
SNP_A-1997922 BB 0.005983 BB 601.523254 945.402100
SNP_A-2000230 AA 0.003169 AA 1693.645752 1190.891479
SNP_A-2000332 AB 0.009194 AB 1921.318604 1720.920410
SNP_A-2000337 AA 0.003254 AA 1359.153564 324.838531
SNP_A-2000342 AA 0.008670 AA 2698.675537 1407.616699
SNP_A-4268173 AA 0.006110 AA 1059.665527 291.077698

Total number of rows: 909622

Table truncated, full table size 46148 Kbytes.




Supplementary file Size Download File type/resource
GSM457700_SH13T_GenomeWideSNP_6_.CEL.gz 28.2 Mb (ftp)(http) CEL
GSM457700_SH13T_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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