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Sample GSM732053 Query DataSets for GSM732053
Status Public on Dec 31, 2011
Title SH14-N normal prostate
Sample type genomic
 
Source name SH14-N
Organism Homo sapiens
Characteristics tissue: normal prostate
individual: SH14
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 standard Affymetrix protocol
 
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 SNP genotype data from prostate cancer patient at diagnosis
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 May 26, 2011
Last update date Dec 31, 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)
GSE29569 High-resolution genome-wide copy-number analysis suggests a monoclonal origin of multi-focal prostate cancer

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 0.002138 AA 3227.679688 1006.781555
SNP_A-1967418 BB 0.004183 BB 311.665009 1048.331909
SNP_A-1969580 BB 0.005257 BB 2014.994507 4383.240234
SNP_A-4263484 AB 0.001943 AB 1884.776611 1239.608032
SNP_A-1978185 AA 0.003044 AA 1263.078735 276.070648
SNP_A-4264431 AB 0.002479 AB 1406.363159 1023.401367
SNP_A-1980898 BB 0.003958 BB 232.270432 1121.248535
SNP_A-1983139 AA 0.002552 AA 2605.375488 854.258606
SNP_A-4265735 AA 0.000854 AA 2050.743164 647.033325
SNP_A-1995832 BB 0.000362 BB 825.355286 2611.892578
SNP_A-1995893 BB 0.001943 BB 707.121155 2964.205078
SNP_A-1997689 BB 0.002871 BB 693.053162 2524.610840
SNP_A-1997709 AA 0.007404 AA 1110.387329 290.900421
SNP_A-1997896 AA 0.001224 AA 1697.496948 596.531189
SNP_A-1997922 NC 0.222151 BB 566.748901 772.251770
SNP_A-2000230 AB 0.001713 AB 1297.452881 1750.390991
SNP_A-2000332 AB 0.001925 AB 2607.739990 2418.172607
SNP_A-2000337 AA 0.006779 AA 1702.891113 260.673523
SNP_A-2000342 AA 0.001572 AA 3108.157959 1109.792358
SNP_A-4268173 AA 0.005103 AA 1678.690430 492.710144

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM732053_SH14-N.CEL.gz 29.9 Mb (ftp)(http) CEL
GSM732053_SH14-N.chp.gz 13.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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