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Sample GSM731951 Query DataSets for GSM731951
Status Public on Dec 31, 2011
Title WX11-TL1 prostate tumour
Sample type genomic
 
Source name WX11-TL1
Organism Homo sapiens
Characteristics tissue: WX11-TL1
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 0.006559 BB 1427.580078 3314.081299
SNP_A-1967418 BB 0.000988 BB 458.841553 1087.467407
SNP_A-1969580 BB 0.001745 BB 1674.553223 3928.949463
SNP_A-4263484 BB 0.006302 BB 735.401001 2062.035400
SNP_A-1978185 AA 0.000843 AA 1553.542603 404.390137
SNP_A-4264431 AB 0.002002 AB 1438.880981 1107.254150
SNP_A-1980898 BB 0.006109 BB 316.295044 1259.781006
SNP_A-1983139 AA 0.002086 AA 1763.058716 607.758789
SNP_A-4265735 AB 0.000287 AB 1454.196289 1472.014404
SNP_A-1995832 AB 0.009705 AB 2093.038086 1495.142090
SNP_A-1995893 AB 0.003047 AB 2038.580200 2110.359375
SNP_A-1997689 BB 0.003222 BB 917.095215 2452.803467
SNP_A-1997709 AA 0.003606 AA 1766.351318 409.113403
SNP_A-1997896 AA 0.004873 AA 1117.212646 688.430786
SNP_A-1997922 AB 0.002684 AB 674.150391 629.937927
SNP_A-2000230 AA 0.006140 AA 1932.935059 1235.925415
SNP_A-2000332 AB 0.001770 AB 1989.458374 2185.804688
SNP_A-2000337 AA 0.001216 AA 1570.327148 448.746094
SNP_A-2000342 AA 0.002803 AA 3179.559570 1364.928955
SNP_A-4268173 AA 0.000155 AA 1433.786255 395.187836

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM731951_WX11-TL1.CEL.gz 25.4 Mb (ftp)(http) CEL
GSM731951_WX11-TL1.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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