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Sample GSM457689 Query DataSets for GSM457689
Status Public on May 15, 2010
Title SH6 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 0.002040 AA 3251.160645 970.109375
SNP_A-1967418 BB 0.005023 BB 422.074554 976.908691
SNP_A-1969580 BB 0.005640 BB 1668.904663 3861.759521
SNP_A-4263484 AB 0.001397 AB 1906.351929 1427.558594
SNP_A-1978185 AA 0.003791 AA 1151.715576 253.682373
SNP_A-4264431 AA 0.001727 AA 2321.869629 561.085205
SNP_A-1980898 BB 0.002532 BB 298.395294 1326.052124
SNP_A-1983139 AB 0.000894 AB 1684.911621 1383.774048
SNP_A-4265735 AB 0.005452 AB 1696.439453 1763.801392
SNP_A-1995832 AB 0.004523 AB 2150.464600 1716.607422
SNP_A-1995893 AB 0.002672 AB 1952.346313 2228.113770
SNP_A-1997689 BB 0.002141 BB 860.937805 2560.113525
SNP_A-1997709 AA 0.020586 AA 1723.129028 412.442749
SNP_A-1997896 AA 0.001771 AA 1632.309204 667.502869
SNP_A-1997922 AB 0.008625 AB 852.590149 635.259827
SNP_A-2000230 AA 0.003013 AA 1826.934326 970.065002
SNP_A-2000332 AB 0.000011 AB 2499.600098 2458.017578
SNP_A-2000337 AA 0.005756 AA 1868.578003 336.731354
SNP_A-2000342 AA 0.002477 AA 3056.805908 1260.473877
SNP_A-4268173 AA 0.001309 AA 1650.044067 358.632599

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.




Supplementary file Size Download File type/resource
GSM457689_SH6_T_GenomeWideSNP_6_.CEL.gz 27.7 Mb (ftp)(http) CEL
GSM457689_SH6_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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