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Sample GSM457754 Query DataSets for GSM457754
Status Public on May 15, 2010
Title P55 UK normal prostate
Sample type genomic
 
Source name UK 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 BB 0.009287 BB 1383.120117 4054.826660
SNP_A-1967418 BB 0.000399 BB 358.522552 949.887573
SNP_A-1969580 BB 0.003009 BB 1497.873901 4757.380371
SNP_A-4263484 AB 0.007610 AB 1214.586182 853.259644
SNP_A-1978185 AA 0.001401 AA 1457.825928 403.920654
SNP_A-4264431 AB 0.005711 AB 1349.038452 845.171936
SNP_A-1980898 AB 0.009397 AB 549.121399 699.298279
SNP_A-1983139 AA 0.003382 AA 3161.500244 985.735413
SNP_A-4265735 AA 0.004849 AA 2195.000244 705.413269
SNP_A-1995832 AB 0.006388 AB 2719.278809 2659.508789
SNP_A-1995893 AB 0.002963 AB 2156.720459 2343.502441
SNP_A-1997689 BB 0.006052 BB 1159.698730 2912.992920
SNP_A-1997709 AA 0.001889 AA 1407.061279 315.393585
SNP_A-1997896 AB 0.003632 AB 1135.634399 1209.933594
SNP_A-1997922 AB 0.014932 AB 658.330078 385.080383
SNP_A-2000230 AA 0.004085 AA 1687.130859 1230.008911
SNP_A-2000332 AB 0.004280 AB 3437.308105 2878.081787
SNP_A-2000337 AA 0.003705 AA 1350.642822 301.010223
SNP_A-2000342 AA 0.017662 AA 2378.003418 419.651154
SNP_A-4268173 AA 0.008410 AA 1566.270752 268.230255

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM457754_P55N_SNP6_GenomeWideSNP_6_.CEL.gz 27.4 Mb (ftp)(http) CEL
GSM457754_P55N_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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