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Sample GSM775347 Query DataSets for GSM775347
Status Public on Dec 31, 2011
Title WX8-PL1 High grade PIN
Sample type genomic
 
Source name WX8-PL
Organism Homo sapiens
Characteristics individual: WX8
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 BB 0.002398 BB 1300.241089 4139.377930
SNP_A-1967418 BB 0.010100 BB 352.208313 1231.282471
SNP_A-1969580 BB 0.005630 BB 1362.224854 3124.645020
SNP_A-4263484 AB 0.017616 AB 2194.991211 1647.686279
SNP_A-1978185 AA 0.002725 AA 1520.008057 443.330231
SNP_A-4264431 AB 0.001085 AB 1409.781494 1134.059937
SNP_A-1980898 BB 0.002139 BB 340.009430 1174.368408
SNP_A-1983139 AA 0.003825 AA 1834.193604 763.349121
SNP_A-4265735 AB 0.005641 AB 1260.857666 1466.783569
SNP_A-1995832 BB 0.001737 BB 788.808472 1968.455200
SNP_A-1995893 BB 0.009092 BB 950.525696 3112.519775
SNP_A-1997689 BB 0.016076 BB 1112.011230 3281.594727
SNP_A-1997709 AA 0.008117 AA 1342.480225 406.011322
SNP_A-1997896 AB 0.001326 AB 909.185791 1182.535400
SNP_A-1997922 AB 0.002936 AB 690.900818 533.858521
SNP_A-2000230 AA 0.003328 AA 1948.974365 1198.738892
SNP_A-2000332 AA 0.005179 AA 3033.374756 639.700623
SNP_A-2000337 AA 0.004404 AA 1830.313721 396.010406
SNP_A-2000342 AA 0.006225 AA 3678.740723 1408.939453
SNP_A-4268173 AB 0.004040 AB 830.423218 944.749878

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.




Supplementary file Size Download File type/resource
GSM775347_WXB8-PL1.CEL.gz 25.3 Mb (ftp)(http) CEL
GSM775347_WXB8-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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