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Sample GSM457744 Query DataSets for GSM457744
Status Public on May 15, 2010
Title SH37 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 0.002625 AA 3185.902588 1338.990967
SNP_A-1967418 BB 0.006150 BB 465.163177 837.206177
SNP_A-1969580 BB 0.067637 BB 2001.177246 3501.615234
SNP_A-4263484 AA 0.006508 AA 2465.009277 761.757751
SNP_A-1978185 AB 0.019377 AB 831.663147 780.873901
SNP_A-4264431 BB 0.001268 BB 733.313599 1487.580444
SNP_A-1980898 BB 0.002185 BB 327.149841 936.272339
SNP_A-1983139 BB 0.009465 BB 1157.367432 2570.528076
SNP_A-4265735 BB 0.002268 BB 967.562866 2039.823486
SNP_A-1995832 AB 0.006652 AB 2157.775879 1837.695068
SNP_A-1995893 AB 0.006637 AB 1932.941772 1942.777710
SNP_A-1997689 BB 0.006608 BB 992.124512 2283.017822
SNP_A-1997709 AA 0.011151 AA 1462.544312 462.841125
SNP_A-1997896 AA 0.012136 AA 1222.887817 784.835999
SNP_A-1997922 AB 0.014206 AB 629.380066 623.909424
SNP_A-2000230 AB 0.005036 AB 1190.907837 1545.238403
SNP_A-2000332 AB 0.000229 AB 2057.305664 2086.603760
SNP_A-2000337 AA 0.008015 AA 1509.609741 451.253693
SNP_A-2000342 AA 0.008206 AA 2572.721680 1338.204346
SNP_A-4268173 AA 0.006535 AA 964.201355 318.617493

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.




Supplementary file Size Download File type/resource
GSM457744_SH37_T_GenomeWideSNP_6_.CEL.gz 27.0 Mb (ftp)(http) CEL
GSM457744_SH37_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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