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Sample GSM775356 Query DataSets for GSM775356
Status Public on Dec 31, 2011
Title WX68-PL1 High grade PIN
Sample type genomic
 
Source name WX68-PL
Organism Homo sapiens
Characteristics individual: WX68
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 AA 0.003495 AA 3359.455811 773.680786
SNP_A-1967418 BB 0.001033 BB 411.575714 1009.582214
SNP_A-1969580 BB 0.003505 BB 1794.229736 4096.445312
SNP_A-4263484 AB 0.001045 AB 1639.905884 1265.868164
SNP_A-1978185 AA 0.004169 AA 1258.325928 383.156036
SNP_A-4264431 AA 0.002388 AA 1699.008545 509.159821
SNP_A-1980898 BB 0.001611 BB 348.288544 1191.434204
SNP_A-1983139 AA 0.001287 AA 1936.501709 680.753967
SNP_A-4265735 AA 0.005174 AA 2054.078125 618.893127
SNP_A-1995832 AA 0.003850 AA 2356.864014 529.962708
SNP_A-1995893 AA 0.004564 AA 2832.827881 1160.103271
SNP_A-1997689 BB 0.002796 BB 785.729187 2576.086426
SNP_A-1997709 AA 0.005481 AA 1839.512207 428.363098
SNP_A-1997896 AA 0.002799 AA 1275.903564 578.848267
SNP_A-1997922 AA 0.002033 AA 832.665833 305.844574
SNP_A-2000230 AA 0.005173 AA 2258.906250 1033.948608
SNP_A-2000332 AA 0.001844 AA 2873.739990 747.168762
SNP_A-2000337 AA 0.008225 AA 1957.282349 385.738129
SNP_A-2000342 AA 0.001513 AA 2869.518311 1163.152100
SNP_A-4268173 AB 0.004437 AB 1081.278687 953.357849

Total number of rows: 909622

Table truncated, full table size 46147 Kbytes.




Supplementary file Size Download File type/resource
GSM775356_WX68-PL1.CEL.gz 24.3 Mb (ftp)(http) CEL
GSM775356_WX68-PL1.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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