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Sample GSM457719 Query DataSets for GSM457719
Status Public on May 15, 2010
Title SH23 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 Apr 18, 2011
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 AB 0.000773 AB 2236.313965 2488.786133
SNP_A-1967418 BB 0.000953 BB 373.619995 1028.575195
SNP_A-1969580 BB 0.002344 BB 1496.593140 4124.545410
SNP_A-4263484 BB 0.000345 BB 588.843262 1958.146973
SNP_A-1978185 AA 0.000945 AA 1155.397217 307.347076
SNP_A-4264431 AA 0.001827 AA 2319.953125 454.151947
SNP_A-1980898 BB 0.002387 BB 309.431702 1357.233643
SNP_A-1983139 AB 0.001437 AB 1608.878784 1236.967773
SNP_A-4265735 BB 0.005998 BB 780.479309 1796.096558
SNP_A-1995832 BB 0.001731 BB 719.364502 2498.977783
SNP_A-1995893 BB 0.006666 BB 677.738159 2599.791504
SNP_A-1997689 BB 0.005841 BB 735.862549 2916.813721
SNP_A-1997709 AA 0.004637 AA 1035.105713 245.672516
SNP_A-1997896 AA 0.009326 AA 2142.063477 724.302979
SNP_A-1997922 BB 0.002649 BB 554.002136 1057.760010
SNP_A-2000230 AB 0.001272 AB 1332.011719 1717.641479
SNP_A-2000332 AB 0.010843 AB 2220.761719 2292.235840
SNP_A-2000337 AA 0.007449 AA 1364.447144 253.346542
SNP_A-2000342 AA 0.003353 AA 3162.342773 1072.089722
SNP_A-4268173 AA 0.002559 AA 1715.552979 462.772766

Total number of rows: 909622

Table truncated, full table size 46149 Kbytes.




Supplementary file Size Download File type/resource
GSM457719_SH23_N_GenomeWideSNP_6_.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM457719_SH23_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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