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Sample GSM457701 Query DataSets for GSM457701
Status Public on May 15, 2010
Title SH14 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 0.006609 AA 2706.089111 904.460083
SNP_A-1967418 BB 0.003909 BB 412.473145 794.241516
SNP_A-1969580 BB 0.004385 BB 1271.390259 3226.401123
SNP_A-4263484 AB 0.005251 AB 1596.480591 1119.586548
SNP_A-1978185 AA 0.001512 AA 1335.279175 358.457428
SNP_A-4264431 AB 0.001158 AB 1370.818848 1037.104980
SNP_A-1980898 BB 0.004461 BB 314.110046 1125.076050
SNP_A-1983139 AA 0.002945 AA 2124.679932 751.539612
SNP_A-4265735 AA 0.008070 AA 1421.415649 631.223877
SNP_A-1995832 BB 0.003396 BB 764.543213 2070.550049
SNP_A-1995893 BB 0.007673 BB 715.940430 2179.232910
SNP_A-1997689 BB 0.000400 BB 962.205750 2549.750732
SNP_A-1997709 AA 0.003972 AA 1045.759766 271.225922
SNP_A-1997896 AA 0.002212 AA 1611.297729 751.980286
SNP_A-1997922 BB 0.007039 BB 682.382507 1054.236084
SNP_A-2000230 AB 0.001656 AB 1378.067139 1626.751953
SNP_A-2000332 AB 0.006693 AB 2316.935547 2371.793457
SNP_A-2000337 AA 0.003104 AA 1352.099487 391.780243
SNP_A-2000342 AA 0.010322 AA 3323.278076 1412.790527
SNP_A-4268173 AA 0.005080 AA 1541.072876 447.128845

Total number of rows: 909622

Table truncated, full table size 46155 Kbytes.




Supplementary file Size Download File type/resource
GSM457701_SH14T_GenomeWideSNP_6_.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM457701_SH14T_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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