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Sample GSM731958 Query DataSets for GSM731958
Status Public on Dec 31, 2011
Title WX21-TR1 prostate tumour
Sample type genomic
 
Source name WX21-TR1
Organism Homo sapiens
Characteristics tissue: prostate tumor
individual: WX21
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 0.003077 BB 836.356018 3134.924072
SNP_A-1967418 AB 0.002940 AB 867.453247 662.265808
SNP_A-1969580 BB 0.003741 BB 1446.322144 4527.811035
SNP_A-4263484 AB 0.009250 AB 1921.370605 1099.868896
SNP_A-1978185 AA 0.008085 AA 1009.890015 384.210480
SNP_A-4264431 AA 0.001011 AA 2944.309082 546.568176
SNP_A-1980898 BB 0.004247 BB 381.516205 1416.148193
SNP_A-1983139 AA 0.001927 AA 2814.810303 960.736877
SNP_A-4265735 AA 0.000765 AA 2930.264648 875.538452
SNP_A-1995832 AB 0.005447 AB 2576.672852 2088.101318
SNP_A-1995893 AB 0.004159 AB 2440.501221 2720.030029
SNP_A-1997689 AB 0.006788 AB 2792.355469 2459.224121
SNP_A-1997709 AB 0.002558 AB 813.211487 867.453247
SNP_A-1997896 AB 0.003162 AB 1240.897095 1801.925049
SNP_A-1997922 AB 0.006536 AB 598.246643 577.484131
SNP_A-2000230 AA 0.001664 AA 2280.222900 1048.346436
SNP_A-2000332 BB 0.001654 BB 1718.490479 5349.454102
SNP_A-2000337 AA 0.002656 AA 1674.883545 455.759003
SNP_A-2000342 AA 0.003825 AA 4696.203613 1334.822144
SNP_A-4268173 AA 0.001746 AA 2195.656982 430.836792

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM731958_WX21-TR1.CEL.gz 28.9 Mb (ftp)(http) CEL
GSM731958_WX21-TR1.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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