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Sample GSM731956 Query DataSets for GSM731956
Status Public on Dec 31, 2011
Title WX12-N normal prostate
Sample type genomic
 
Source name WX12-N
Organism Homo sapiens
Characteristics tissue: normal prostate
individual: WX12
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 AB 0.003288 AB 1727.568848 1768.973145
SNP_A-1967418 AB 0.002876 AB 680.901123 546.059021
SNP_A-1969580 BB 0.000698 BB 1856.798584 5498.143555
SNP_A-4263484 BB 0.005790 BB 443.708649 1611.299561
SNP_A-1978185 AA 0.004963 AA 1220.514038 244.349838
SNP_A-4264431 AA 0.004026 AA 3065.925293 684.887451
SNP_A-1980898 BB 0.000093 BB 360.056488 1575.543335
SNP_A-1983139 AA 0.000868 AA 3036.804199 983.612549
SNP_A-4265735 AA 0.003617 AA 2411.646484 777.798401
SNP_A-1995832 AB 0.002835 AB 1824.679932 1724.461914
SNP_A-1995893 AB 0.001923 AB 1799.901123 2105.221191
SNP_A-1997689 BB 0.006922 BB 650.966736 2251.053711
SNP_A-1997709 AA 0.000711 AA 1438.855103 326.045410
SNP_A-1997896 AA 0.010442 AA 2541.358887 709.014282
SNP_A-1997922 AB 0.007544 AB 569.204773 687.392517
SNP_A-2000230 AA 0.002623 AA 2552.639160 1006.375671
SNP_A-2000332 AB 0.000824 AB 3009.228027 2868.917236
SNP_A-2000337 AA 0.003477 AA 1483.527100 317.109802
SNP_A-2000342 AA 0.003371 AA 3753.143066 1332.027588
SNP_A-4268173 AA 0.000788 AA 2238.278320 491.128754

Total number of rows: 909622

Table truncated, full table size 46159 Kbytes.




Supplementary file Size Download File type/resource
GSM731956_WX12-N.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM731956_WX12-N.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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