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Sample GSM457682 Query DataSets for GSM457682
Status Public on May 15, 2010
Title SH2 Chinese normal prostate
Sample type genomic
 
Source name Chinese normal prostate
Organism Homo sapiens
Characteristics tissue: Normal prostate
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 0.004800 AA 3447.483643 1005.686096
SNP_A-1967418 BB 0.005422 BB 363.367920 843.244385
SNP_A-1969580 BB 0.001305 BB 1381.320068 3431.370361
SNP_A-4263484 NC 0.152617 AA 2270.443604 484.906372
SNP_A-1978185 AA 0.006516 AA 1310.342041 307.470306
SNP_A-4264431 AA 0.004013 AA 1962.902710 495.486389
SNP_A-1980898 BB 0.003641 BB 283.949310 1138.999634
SNP_A-1983139 AA 0.000684 AA 2344.231201 871.335144
SNP_A-4265735 AB 0.010890 AB 731.388489 2064.997559
SNP_A-1995832 AB 0.004848 AB 1762.526367 1456.735107
SNP_A-1995893 AB 0.004541 AB 1858.808960 2151.669922
SNP_A-1997689 BB 0.001039 BB 926.701050 3165.168213
SNP_A-1997709 AA 0.010691 AA 1493.256226 295.372375
SNP_A-1997896 AA 0.000288 AA 1516.433838 621.242859
SNP_A-1997922 AB 0.001110 AB 794.643311 724.475891
SNP_A-2000230 AB 0.008276 AB 1405.174683 2215.437988
SNP_A-2000332 BB 0.013683 BB 1343.895874 2701.481201
SNP_A-2000337 AA 0.005189 AA 1322.907104 290.229797
SNP_A-2000342 AA 0.030043 AA 3025.185791 1275.338745
SNP_A-4268173 AA 0.002100 AA 1358.256592 317.971313

Total number of rows: 909622

Table truncated, full table size 46142 Kbytes.




Supplementary file Size Download File type/resource
GSM457682_SH2_N_SNP6_GenomeWideSNP_6_.CEL.gz 31.6 Mb (ftp)(http) CEL
GSM457682_SH2_N_SNP6_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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