NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM457711 Query DataSets for GSM457711
Status Public on May 15, 2010
Title SH19 Chinese prostate cancer
Sample type genomic
 
Source name Chinese prostate cancer
Organism Homo sapiens
Characteristics tissue: Prostate cancer
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 AA 0.001587 AA 3561.812988 1061.772095
SNP_A-1967418 BB 0.031899 BB 333.752106 1478.185059
SNP_A-1969580 BB 0.000967 BB 1683.810181 4369.213867
SNP_A-4263484 AB 0.002624 AB 1778.147827 1317.721558
SNP_A-1978185 AA 0.010927 AA 1504.808350 383.149750
SNP_A-4264431 AB 0.012938 AB 1842.425537 1363.925171
SNP_A-1980898 BB 0.004478 BB 351.131561 1384.472046
SNP_A-1983139 AB 0.004092 AB 1574.754272 1105.077515
SNP_A-4265735 BB 0.001975 BB 835.927368 1990.885498
SNP_A-1995832 AB 0.006563 AB 2230.242432 1689.033936
SNP_A-1995893 AB 0.006812 AB 1826.847046 2016.920532
SNP_A-1997689 BB 0.009273 BB 1039.043579 2943.130371
SNP_A-1997709 AA 0.002598 AA 1208.868042 228.091461
SNP_A-1997896 AA 0.001937 AA 1681.559692 657.733032
SNP_A-1997922 AB 0.002426 AB 756.321228 675.254456
SNP_A-2000230 AA 0.004839 AA 2178.228516 1071.049072
SNP_A-2000332 AB 0.004800 AB 2500.937988 2282.615479
SNP_A-2000337 AA 0.006030 AA 1594.498291 410.322113
SNP_A-2000342 AA 0.015570 AA 3659.268066 1220.161255
SNP_A-4268173 AA 0.006385 AA 1953.964966 360.530457

Total number of rows: 909622

Table truncated, full table size 46151 Kbytes.




Supplementary file Size Download File type/resource
GSM457711_SH19_T_GenomeWideSNP_6_.CEL.gz 28.3 Mb (ftp)(http) CEL
GSM457711_SH19_T_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