NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM457686 Query DataSets for GSM457686
Status Public on May 15, 2010
Title SH4 Chinese normal prostate
Sample type genomic
 
Source name Chinese normal prostate
Organism Homo sapiens
Characteristics tissue: Normal prostate
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 Hybridized to human SNP 6.0 array
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 Sep 29, 2009
Last update date Mar 05, 2010
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)
GSE18333 Distinct genomic differences in prostate cancer between Western countries and China

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 AB 0.003245 AB 3034.067871 3172.800049
SNP_A-1967418 AB 0.005086 AB 618.463135 520.230713
SNP_A-1969580 BB 0.001777 BB 1370.427490 3504.735840
SNP_A-4263484 AA 0.013242 AA 2604.712891 564.873901
SNP_A-1978185 AB 0.008799 AB 1002.453491 1060.865112
SNP_A-4264431 BB 0.003693 BB 645.971680 1380.171997
SNP_A-1980898 AB 0.006411 AB 591.850952 470.679047
SNP_A-1983139 AA 0.017503 AA 2541.189453 945.844910
SNP_A-4265735 NC 0.409059 AA 1416.049438 1460.458984
SNP_A-1995832 AB 0.006439 AB 2044.923096 1682.246094
SNP_A-1995893 AB 0.009700 AB 2439.469482 2522.270020
SNP_A-1997689 BB 0.001847 BB 1112.153687 3597.107422
SNP_A-1997709 AA 0.000763 AA 1750.166382 318.007935
SNP_A-1997896 AA 0.001852 AA 1392.244873 661.684387
SNP_A-1997922 AB 0.005408 AB 711.808777 578.035583
SNP_A-2000230 AB 0.004208 AB 1538.757202 1917.680298
SNP_A-2000332 AB 0.001481 AB 2374.164551 2417.101318
SNP_A-2000337 AA 0.007195 AA 1518.983276 353.200592
SNP_A-2000342 AA 0.007093 AA 3607.780029 1442.653442
SNP_A-4268173 AA 0.003436 AA 1152.826904 306.398254

Total number of rows: 909622

Table truncated, full table size 46116 Kbytes.




Supplementary file Size Download File type/resource
GSM457686_SH4_N_SNP6_GenomeWideSNP_6_.CEL.gz 31.1 Mb (ftp)(http) CEL
GSM457686_SH4_N_SNP6_GenomeWideSNP_6_.birdseed-v2.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