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Sample GSM731955 Query DataSets for GSM731955
Status Public on Dec 31, 2011
Title WX12-TL2 prostate tumour
Sample type genomic
 
Source name WX12-TL2
Organism Homo sapiens
Characteristics tissue: WX12-TL2
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 0.002447 AB 2073.681396 1974.211182
SNP_A-1967418 AB 0.012516 AB 985.506653 704.038086
SNP_A-1969580 BB 0.001301 BB 1580.813965 5102.791992
SNP_A-4263484 BB 0.003483 BB 602.972107 1817.100586
SNP_A-1978185 AA 0.003858 AA 1504.103271 373.769989
SNP_A-4264431 AA 0.003830 AA 2478.123047 492.749420
SNP_A-1980898 BB 0.001730 BB 307.110474 1402.002441
SNP_A-1983139 AA 0.004651 AA 3469.034668 1195.898804
SNP_A-4265735 AA 0.000206 AA 2808.625000 860.641357
SNP_A-1995832 AB 0.003277 AB 1929.969604 1484.317383
SNP_A-1995893 AB 0.003680 AB 1786.766235 1961.920288
SNP_A-1997689 BB 0.005312 BB 992.085876 3207.512451
SNP_A-1997709 AA 0.000625 AA 1527.693604 318.751923
SNP_A-1997896 AA 0.000821 AA 1961.259888 587.189941
SNP_A-1997922 AB 0.004043 AB 924.097046 747.235779
SNP_A-2000230 AA 0.002258 AA 2113.890869 852.414246
SNP_A-2000332 AB 0.000836 AB 3105.460449 3009.232422
SNP_A-2000337 AA 0.005219 AA 2031.380615 339.174713
SNP_A-2000342 AA 0.002593 AA 4558.142090 1382.756470
SNP_A-4268173 AA 0.000618 AA 2080.566650 420.587280

Total number of rows: 909622

Table truncated, full table size 46158 Kbytes.




Supplementary file Size Download File type/resource
GSM731955_WX12-TL2.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM731955_WX12-TL2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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