NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM732032 Query DataSets for GSM732032
Status Public on Dec 31, 2011
Title SH12-T1 prostate tumour
Sample type genomic
 
Source name SH12-T1
Organism Homo sapiens
Characteristics tissue: SH12-T1
individual: SH12
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 0.006739 AA 4029.048340 1400.491089
SNP_A-1967418 BB 0.005065 BB 464.833954 857.164856
SNP_A-1969580 BB 0.006803 BB 1258.308228 3008.514893
SNP_A-4263484 AB 0.002567 AB 1619.247681 1180.671997
SNP_A-1978185 AA 0.007540 AA 1315.411133 453.629028
SNP_A-4264431 AB 0.010459 AB 1246.392578 865.132751
SNP_A-1980898 BB 0.005621 BB 348.713196 897.297180
SNP_A-1983139 AA 0.005257 AA 2561.325439 1106.279297
SNP_A-4265735 AA 0.001901 AA 1891.849487 777.675110
SNP_A-1995832 AB 0.002904 AB 1891.823608 1446.876587
SNP_A-1995893 AB 0.001253 AB 1814.471069 2164.439453
SNP_A-1997689 BB 0.006116 BB 1076.674683 2900.149170
SNP_A-1997709 AA 0.005599 AA 1718.772705 364.426880
SNP_A-1997896 AA 0.005200 AA 1398.199829 620.091980
SNP_A-1997922 AB 0.001124 AB 804.325745 723.817627
SNP_A-2000230 AA 0.015647 AA 1864.050537 1418.826782
SNP_A-2000332 AB 0.002080 AB 2179.664551 2149.711670
SNP_A-2000337 AA 0.024269 AA 1251.886353 495.950684
SNP_A-2000342 AA 0.000664 AA 2887.908203 1292.187134
SNP_A-4268173 AB 0.002663 AB 759.370667 772.044678

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.




Supplementary file Size Download File type/resource
GSM732032_SH12-T1.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM732032_SH12-T1.chp.gz 13.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap