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Sample GSM731953 Query DataSets for GSM731953
Status Public on Dec 31, 2011
Title WX11-N normal prostate
Sample type genomic
 
Source name WX11-N
Organism Homo sapiens
Characteristics tissue: normal prostate
individual: WX11
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 standard Affymetrix protocol
 
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 SNP genotype data from prostate cancer patient at diagnosis
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 May 26, 2011
Last update date Dec 31, 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)
GSE29569 High-resolution genome-wide copy-number analysis suggests a monoclonal origin of multi-focal prostate cancer

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 0.015618 BB 1761.013794 3520.163574
SNP_A-1967418 BB 0.014469 BB 419.806366 780.111938
SNP_A-1969580 BB 0.001561 BB 1431.840576 3449.451416
SNP_A-4263484 BB 0.001573 BB 582.058044 1715.480835
SNP_A-1978185 AA 0.005263 AA 1652.196899 462.713562
SNP_A-4264431 AB 0.001699 AB 1266.215576 1011.055359
SNP_A-1980898 BB 0.012893 BB 462.813416 1108.491577
SNP_A-1983139 AA 0.003675 AA 1471.937256 587.838989
SNP_A-4265735 AB 0.010562 AB 1345.880127 1703.150757
SNP_A-1995832 AB 0.002586 AB 1692.628052 1245.434204
SNP_A-1995893 AB 0.002194 AB 1737.868774 1808.810791
SNP_A-1997689 BB 0.008140 BB 909.033203 2255.281982
SNP_A-1997709 AA 0.004348 AA 1745.547485 424.435394
SNP_A-1997896 AA 0.003734 AA 1184.992310 518.608032
SNP_A-1997922 AB 0.003038 AB 693.430725 534.134277
SNP_A-2000230 AA 0.005621 AA 2284.602051 1260.288574
SNP_A-2000332 AB 0.004528 AB 2227.448242 2147.608154
SNP_A-2000337 AA 0.006864 AA 1209.881348 401.260040
SNP_A-2000342 AA 0.003457 AA 3464.011475 1297.487183
SNP_A-4268173 AA 0.001701 AA 1371.620483 355.819366

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.




Supplementary file Size Download File type/resource
GSM731953_WX11-N.CEL.gz 24.7 Mb (ftp)(http) CEL
GSM731953_WX11-N.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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