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Sample GSM457715 Query DataSets for GSM457715
Status Public on May 15, 2010
Title SH21 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 0.002231 AA 3574.076172 1094.119995
SNP_A-1967418 BB 0.000929 BB 345.171265 957.101807
SNP_A-1969580 BB 0.004423 BB 1700.407471 4619.348633
SNP_A-4263484 AB 0.002892 AB 2067.704346 1403.603271
SNP_A-1978185 AA 0.004813 AA 1066.034668 348.414673
SNP_A-4264431 AB 0.004779 AB 1387.423828 944.974243
SNP_A-1980898 BB 0.003846 BB 236.909409 1054.323975
SNP_A-1983139 BB 0.002856 BB 544.917908 1931.906128
SNP_A-4265735 BB 0.004551 BB 654.713379 1952.222900
SNP_A-1995832 BB 0.003200 BB 667.639954 2330.786621
SNP_A-1995893 BB 0.001573 BB 684.651306 3041.283936
SNP_A-1997689 BB 0.003276 BB 747.417114 2822.043213
SNP_A-1997709 AA 0.001874 AA 1190.006714 250.239212
SNP_A-1997896 AA 0.003175 AA 1812.871094 704.285706
SNP_A-1997922 BB 0.002441 BB 514.392029 934.445557
SNP_A-2000230 AA 0.002656 AA 1920.426270 1010.374878
SNP_A-2000332 AA 0.009221 AA 3130.704346 672.866943
SNP_A-2000337 AA 0.005688 AA 1382.597778 305.597443
SNP_A-2000342 AA 0.006535 AA 3341.857422 1309.505371
SNP_A-4268173 AA 0.001080 AA 1610.090210 386.975647

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM457715_SH21_T_GenomeWideSNP_6_.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM457715_SH21_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

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