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Sample GSM775354 Query DataSets for GSM775354
Status Public on Dec 31, 2011
Title WX47-PL1 High grade PIN
Sample type genomic
 
Source name WX47-PL
Organism Homo sapiens
Characteristics individual: WX47
tissue: Prostate tissue
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 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 Aug 09, 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 0.002575 AB 2039.556030 1927.476562
SNP_A-1967418 AB 0.005281 AB 619.776855 599.316345
SNP_A-1969580 BB 0.003082 BB 2051.804443 5500.525879
SNP_A-4263484 BB 0.004336 BB 443.166260 1755.212524
SNP_A-1978185 AA 0.005510 AA 1068.609619 246.135605
SNP_A-4264431 AB 0.005546 AB 1942.358276 1690.580811
SNP_A-1980898 AB 0.002499 AB 941.718384 803.017212
SNP_A-1983139 AA 0.006267 AA 3094.227539 726.269958
SNP_A-4265735 AA 0.002318 AA 2519.861572 793.508118
SNP_A-1995832 AA 0.006258 AA 2618.483398 731.849854
SNP_A-1995893 AA 0.000729 AA 3270.492676 1221.427368
SNP_A-1997689 BB 0.003708 BB 739.507690 2549.421143
SNP_A-1997709 AA 0.003586 AA 1843.612793 353.102936
SNP_A-1997896 AA 0.003714 AA 1716.708862 641.648254
SNP_A-1997922 AA 0.004764 AA 825.989136 261.402374
SNP_A-2000230 AA 0.000740 AA 2434.868652 1015.408997
SNP_A-2000332 AA 0.006648 AA 4788.870117 718.370361
SNP_A-2000337 AA 0.002999 AA 1892.900757 413.135315
SNP_A-2000342 AA 0.003482 AA 3885.199463 1406.016113
SNP_A-4268173 AB 0.000911 AB 1022.246521 839.986694

Total number of rows: 909622

Table truncated, full table size 46152 Kbytes.




Supplementary file Size Download File type/resource
GSM775354_WX47-PL1.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM775354_WX47-PL1.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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