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Sample GSM731977 Query DataSets for GSM731977
Status Public on Dec 31, 2011
Title WX92-TL2 prostate tumour
Sample type genomic
 
Source name WX92-TL2
Organism Homo sapiens
Characteristics tissue: WX92-TL2
individual: WX92
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 0.004077 AB 2349.901611 2477.808105
SNP_A-1967418 BB 0.002525 BB 311.948639 1076.053711
SNP_A-1969580 BB 0.002749 BB 1951.191284 5970.693848
SNP_A-4263484 AB 0.009020 AB 2237.599609 1379.661377
SNP_A-1978185 AA 0.006592 AA 930.400513 339.422638
SNP_A-4264431 AA 0.003063 AA 3780.611572 658.671143
SNP_A-1980898 AB 0.001279 AB 1052.270752 1037.125244
SNP_A-1983139 AA 0.002425 AA 3498.063965 1081.616821
SNP_A-4265735 AB 0.003719 AB 2066.117920 2128.347168
SNP_A-1995832 AB 0.002473 AB 2285.068848 2195.170898
SNP_A-1995893 AB 0.008493 AB 2763.443604 2914.042480
SNP_A-1997689 BB 0.004322 BB 843.286377 2673.153564
SNP_A-1997709 AA 0.009360 AA 1436.308350 191.461594
SNP_A-1997896 AA 0.001723 AA 2150.609131 686.596985
SNP_A-1997922 AB 0.002449 AB 885.417114 885.272522
SNP_A-2000230 AA 0.006731 AA 1768.259155 731.347656
SNP_A-2000332 AA 0.008275 AA 3512.790527 689.354980
SNP_A-2000337 AA 0.003239 AA 1512.754761 448.127228
SNP_A-2000342 AA 0.005413 AA 3838.884766 1023.035095
SNP_A-4268173 AA 0.001901 AA 1684.279541 253.126999

Total number of rows: 909622

Table truncated, full table size 46153 Kbytes.




Supplementary file Size Download File type/resource
GSM731977_WX92-TL2.CEL.gz 27.8 Mb (ftp)(http) CEL
GSM731977_WX92-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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