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Sample GSM457680 Query DataSets for GSM457680
Status Public on May 15, 2010
Title SH1 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 0.016907 AA 2445.208252 787.822144
SNP_A-1967418 BB 0.030707 BB 297.466614 830.850403
SNP_A-1969580 AB 0.076774 AB 1438.221191 2836.758057
SNP_A-4263484 NC 0.195004 AB 505.726715 1501.451904
SNP_A-1978185 AA 0.047765 AA 1150.533813 1352.454956
SNP_A-4264431 NC 0.167415 AB 1138.234497 949.155457
SNP_A-1980898 AB 0.029667 AB 923.209839 786.258728
SNP_A-1983139 NC 0.196403 AB 1203.071289 1109.073853
SNP_A-4265735 NC 0.196394 BB 586.577209 1534.791870
SNP_A-1995832 BB 0.005104 BB 712.842896 2525.370361
SNP_A-1995893 NC 0.185303 BB 712.844055 2634.520020
SNP_A-1997689 NC 0.111059 BB 937.168640 2256.990234
SNP_A-1997709 AA 0.004462 AA 1284.602417 229.474640
SNP_A-1997896 AA 0.062221 AA 1472.291748 565.354736
SNP_A-1997922 BB 0.036536 BB 471.064392 899.333313
SNP_A-2000230 NC 1.000000 BB 1563.824829 1303.760986
SNP_A-2000332 NC 0.181692 AA 2913.239502 1075.206177
SNP_A-2000337 NC 0.196121 BB 1380.139038 372.012939
SNP_A-2000342 NC 0.191165 AA 2493.311768 1106.102905
SNP_A-4268173 NC 0.101438 AA 1290.391602 352.136963

Total number of rows: 909622

Table truncated, full table size 46141 Kbytes.




Supplementary file Size Download File type/resource
GSM457680_SH1_N_SNP6_GenomeWideSNP_6_.CEL.gz 32.4 Mb (ftp)(http) CEL
GSM457680_SH1_N_SNP6_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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