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Sample GSM457706 Query DataSets for GSM457706
Status Public on May 15, 2010
Title SH16 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 AA 0.003597 AA 3356.038086 817.327698
SNP_A-1967418 BB 0.001525 BB 364.051208 1073.992065
SNP_A-1969580 BB 0.002964 BB 1940.701294 4514.226562
SNP_A-4263484 AB 0.005588 AB 1725.644165 1167.606689
SNP_A-1978185 AB 0.003837 AB 926.045349 883.512573
SNP_A-4264431 BB 0.007459 BB 884.669006 1889.274292
SNP_A-1980898 NC 0.177792 AA 1043.802490 471.919037
SNP_A-1983139 AB 0.002033 AB 1722.910156 1246.464966
SNP_A-4265735 AB 0.012489 AB 1693.927490 1260.286499
SNP_A-1995832 BB 0.011093 BB 700.748352 2925.324707
SNP_A-1995893 BB 0.000260 BB 662.009094 2883.809082
SNP_A-1997689 BB 0.000944 BB 818.669189 2787.762939
SNP_A-1997709 AA 0.006621 AA 944.680908 233.140076
SNP_A-1997896 AA 0.011656 AA 1700.135376 449.035278
SNP_A-1997922 BB 0.003583 BB 578.589844 930.595276
SNP_A-2000230 AA 0.019859 AA 2515.188232 1263.850220
SNP_A-2000332 AA 0.029217 AA 2893.950195 1185.171143
SNP_A-2000337 AA 0.009620 AA 1798.254395 278.987152
SNP_A-2000342 AA 0.012402 AA 3432.690186 1384.628662
SNP_A-4268173 AA 0.029331 AA 1936.946777 685.538635

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM457706_SH16_N_GenomeWideSNP_6_.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM457706_SH16_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

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