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Sample GSM775359 Query DataSets for GSM775359
Status Public on Dec 31, 2011
Title WX92-PL1 High grade PIN
Sample type genomic
 
Source name WX92-PL
Organism Homo sapiens
Characteristics individual: WX92
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 0.006140 AB 1741.618896 2537.113037
SNP_A-1967418 BB 0.010809 BB 217.419159 1081.589844
SNP_A-1969580 BB 0.005382 BB 1706.862305 5974.094238
SNP_A-4263484 AB 0.003713 AB 1586.766846 1217.118652
SNP_A-1978185 AA 0.010427 AA 780.010132 261.228027
SNP_A-4264431 AA 0.009818 AA 3585.743896 418.307251
SNP_A-1980898 AB 0.002247 AB 1118.707153 1060.300659
SNP_A-1983139 AA 0.004031 AA 2571.176025 692.298035
SNP_A-4265735 AB 0.001452 AB 1633.625977 1708.725220
SNP_A-1995832 AB 0.004456 AB 1702.518433 1432.549683
SNP_A-1995893 AB 0.006730 AB 2399.808105 2273.833252
SNP_A-1997689 BB 0.003943 BB 534.081421 2875.347412
SNP_A-1997709 AA 0.000713 AA 1346.235474 294.137421
SNP_A-1997896 AA 0.004019 AA 2133.708496 552.434753
SNP_A-1997922 AB 0.002117 AB 834.135376 714.172241
SNP_A-2000230 AA 0.004909 AA 2146.983398 742.462769
SNP_A-2000332 AA 0.014870 AA 4969.932617 605.988953
SNP_A-2000337 AA 0.002489 AA 1517.726318 335.619080
SNP_A-2000342 AA 0.015256 AA 4698.579590 950.749939
SNP_A-4268173 AA 0.004900 AA 2339.423584 414.788879

Total number of rows: 909622

Table truncated, full table size 46160 Kbytes.




Supplementary file Size Download File type/resource
GSM775359_WX92-PL1.CEL.gz 27.7 Mb (ftp)(http) CEL
GSM775359_WX92-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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