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Sample GSM457684 Query DataSets for GSM457684
Status Public on May 15, 2010
Title SH3 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 BB 0.003424 BB 1336.828247 4015.866943
SNP_A-1967418 AB 0.001488 AB 663.115356 665.912354
SNP_A-1969580 BB 0.035685 BB 1922.194458 3844.171387
SNP_A-4263484 AA 0.007161 AA 3038.655762 614.629089
SNP_A-1978185 AB 0.000731 AB 904.510986 953.263550
SNP_A-4264431 BB 0.005139 BB 699.489136 2005.377441
SNP_A-1980898 BB 0.013377 BB 355.749359 896.076843
SNP_A-1983139 AB 0.009617 AB 2116.156250 1773.354126
SNP_A-4265735 AB 0.007136 AB 1834.468994 1670.932861
SNP_A-1995832 BB 0.002393 BB 961.123352 2859.404541
SNP_A-1995893 BB 0.011646 BB 878.621033 3024.622070
SNP_A-1997689 BB 0.009526 BB 751.531860 2048.121338
SNP_A-1997709 AA 0.002537 AA 1413.321167 310.131134
SNP_A-1997896 AA 0.009805 AA 1324.993408 693.462708
SNP_A-1997922 BB 0.002694 BB 534.193481 857.810547
SNP_A-2000230 AA 0.002698 AA 1907.137573 1207.012085
SNP_A-2000332 AB 0.003276 AB 2347.582520 2315.124268
SNP_A-2000337 AA 0.004984 AA 1601.911377 256.499725
SNP_A-2000342 AA 0.014127 AA 3581.690430 1074.175781
SNP_A-4268173 AA 0.009252 AA 1076.964111 260.960693

Total number of rows: 909622

Table truncated, full table size 46129 Kbytes.




Supplementary file Size Download File type/resource
GSM457684_SH3_N_GenomeWideSNP_6_.CEL.gz 27.7 Mb (ftp)(http) CEL
GSM457684_SH3_N_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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