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Sample GSM731970 Query DataSets for GSM731970
Status Public on Dec 31, 2011
Title WX73-TL1 prostate tumour
Sample type genomic
 
Source name WX73-TL1
Organism Homo sapiens
Characteristics tissue: WX73-TL1
individual: WX73
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 BB 0.004042 BB 968.005066 4256.245117
SNP_A-1967418 BB 0.021814 BB 427.454529 1632.603882
SNP_A-1969580 BB 0.003090 BB 1861.339844 5947.379883
SNP_A-4263484 BB 0.002664 BB 785.661560 2371.531250
SNP_A-1978185 AA 0.002084 AA 1122.876221 302.037170
SNP_A-4264431 AA 0.008681 AA 4381.159180 699.348694
SNP_A-1980898 BB 0.004624 BB 489.192810 1822.825073
SNP_A-1983139 AA 0.007237 AA 3678.965576 1288.632202
SNP_A-4265735 AA 0.007636 AA 3424.552734 937.582642
SNP_A-1995832 AB 0.001648 AB 2162.300293 2071.617432
SNP_A-1995893 AB 0.015377 AB 2582.794678 3428.383301
SNP_A-1997689 BB 0.000914 BB 708.525940 3143.062256
SNP_A-1997709 AA 0.001184 AA 1448.671021 335.867188
SNP_A-1997896 AA 0.002239 AA 2090.736084 594.286255
SNP_A-1997922 AB 0.007204 AB 758.788513 920.636536
SNP_A-2000230 AA 0.001958 AA 2132.868896 874.025269
SNP_A-2000332 AB 0.010853 AB 3379.987549 3726.998535
SNP_A-2000337 AA 0.001552 AA 1552.221436 396.010071
SNP_A-2000342 AA 0.004762 AA 4141.974609 1058.058838
SNP_A-4268173 AA 0.000865 AA 1876.875732 347.223999

Total number of rows: 909622

Table truncated, full table size 46149 Kbytes.




Supplementary file Size Download File type/resource
GSM731970_WX73-TL1.CEL.gz 27.3 Mb (ftp)(http) CEL
GSM731970_WX73-TL1.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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