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Sample GSM775348 Query DataSets for GSM775348
Status Public on Dec 31, 2011
Title WX8-PR1 High grade PIN
Sample type genomic
 
Source name WX8-PR
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 0.003919 BB 1210.701416 4185.375488
SNP_A-1967418 BB 0.019124 BB 507.597351 902.479004
SNP_A-1969580 BB 0.009773 BB 1038.576660 3051.964111
SNP_A-4263484 AB 0.003996 AB 1573.364258 1129.612061
SNP_A-1978185 AA 0.006259 AA 1178.911377 385.227844
SNP_A-4264431 AB 0.004331 AB 1202.163940 915.025330
SNP_A-1980898 BB 0.005883 BB 435.106720 1170.958984
SNP_A-1983139 AA 0.006198 AA 1809.232910 555.317566
SNP_A-4265735 AB 0.004513 AB 1353.791382 1262.115601
SNP_A-1995832 BB 0.011038 BB 943.610657 1794.251221
SNP_A-1995893 BB 0.006949 BB 546.243164 2810.211426
SNP_A-1997689 BB 0.004658 BB 1015.251831 2948.661377
SNP_A-1997709 AA 0.007668 AA 1537.265137 301.817627
SNP_A-1997896 AB 0.006594 AB 1065.341431 1092.203735
SNP_A-1997922 AB 0.002940 AB 637.310181 526.092590
SNP_A-2000230 AA 0.003918 AA 1967.102783 1218.366333
SNP_A-2000332 AA 0.001704 AA 2839.384521 816.025635
SNP_A-2000337 AA 0.001396 AA 1484.510864 428.929718
SNP_A-2000342 AA 0.004257 AA 2878.163818 1055.278320
SNP_A-4268173 AB 0.005322 AB 903.175293 742.709900

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM775348_WXB8-PR1.CEL.gz 23.5 Mb (ftp)(http) CEL
GSM775348_WXB8-PR1.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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