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Sample GSM732063 Query DataSets for GSM732063
Status Public on Dec 31, 2011
Title SH17-T2 prostate tumour
Sample type genomic
 
Source name SH17-T2
Organism Homo sapiens
Characteristics tissue: SH17-T2
individual: SH17
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 AA 0.002011 AA 3358.342773 1086.469971
SNP_A-1967418 BB 0.002009 BB 379.075165 1084.133301
SNP_A-1969580 BB 0.004238 BB 1982.949463 4678.587402
SNP_A-4263484 AB 0.021654 AB 2183.361328 1748.718140
SNP_A-1978185 AA 0.000525 AA 1199.456055 304.084290
SNP_A-4264431 AB 0.010064 AB 1798.277710 1284.796753
SNP_A-1980898 BB 0.003019 BB 330.982971 1205.959839
SNP_A-1983139 AA 0.005990 AA 3053.880859 1180.156860
SNP_A-4265735 AA 0.013339 AA 2490.879883 774.697754
SNP_A-1995832 AB 0.007993 AB 2405.695312 2094.039307
SNP_A-1995893 AB 0.012681 AB 2454.497803 2625.897461
SNP_A-1997689 BB 0.003022 BB 881.974792 2653.345215
SNP_A-1997709 AA 0.017417 AA 1716.422485 359.709991
SNP_A-1997896 AA 0.006289 AA 1740.698364 743.662048
SNP_A-1997922 AB 0.002037 AB 738.963806 637.381897
SNP_A-2000230 AA 0.008935 AA 2264.999268 1007.959045
SNP_A-2000332 AA 0.019694 AA 3953.089600 788.808655
SNP_A-2000337 AA 0.013817 AA 1816.948486 252.928146
SNP_A-2000342 AA 0.013684 AA 3320.722656 1426.724487
SNP_A-4268173 AA 0.005101 AA 1691.853760 495.403931

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.




Supplementary file Size Download File type/resource
GSM732063_SH17-T2.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM732063_SH17-T2.chp.gz 13.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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