NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM457688 Query DataSets for GSM457688
Status Public on May 15, 2010
Title SH5 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 0.004103 AB 2520.736572 2119.377441
SNP_A-1967418 AB 0.007036 AB 545.108887 663.109924
SNP_A-1969580 BB 0.003948 BB 1807.320557 4058.670166
SNP_A-4263484 AA 0.004152 AA 2463.307129 640.189331
SNP_A-1978185 AB 0.011018 AB 736.794067 691.744141
SNP_A-4264431 BB 0.003350 BB 853.315979 1802.590210
SNP_A-1980898 AB 0.011331 AB 721.164062 940.510864
SNP_A-1983139 AA 0.044771 AA 2205.253174 1039.203491
SNP_A-4265735 AB 0.008654 AB 1372.261719 1798.412354
SNP_A-1995832 AB 0.004409 AB 1870.777954 1843.994629
SNP_A-1995893 AB 0.009410 AB 1900.204956 2376.860596
SNP_A-1997689 BB 0.002816 BB 710.979858 2521.111328
SNP_A-1997709 AA 0.008434 AA 1759.461548 273.283630
SNP_A-1997896 AA 0.001601 AA 1584.672607 599.110229
SNP_A-1997922 AB 0.003216 AB 631.598999 582.244202
SNP_A-2000230 AB 0.006459 AB 1654.388550 1771.406494
SNP_A-2000332 AB 0.002153 AB 2601.620117 2374.593018
SNP_A-2000337 AA 0.004797 AA 1406.904785 299.704712
SNP_A-2000342 AA 0.001209 AA 3124.203857 1134.515503
SNP_A-4268173 AA 0.003731 AA 1573.304688 300.446350

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.




Supplementary file Size Download File type/resource
GSM457688_SH5_N_GenomeWideSNP_6_.CEL.gz 28.4 Mb (ftp)(http) CEL
GSM457688_SH5_N_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