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Sample GSM731961 Query DataSets for GSM731961
Status Public on Dec 31, 2011
Title WX33-TL2 prostate tumour
Sample type genomic
 
Source name WX33-TL2
Organism Homo sapiens
Characteristics tissue: WX33-TL2
individual: WX33
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 BB 0.007906 BB 602.712158 3416.297363
SNP_A-1967418 BB 0.006448 BB 287.043640 747.943054
SNP_A-1969580 BB 0.004706 BB 1316.400635 4434.872559
SNP_A-4263484 AB 0.004697 AB 1614.089355 1065.718506
SNP_A-1978185 AA 0.001265 AA 1252.672485 342.199646
SNP_A-4264431 AA 0.004135 AA 2813.557617 422.460144
SNP_A-1980898 BB 0.003380 BB 276.369232 1276.640503
SNP_A-1983139 AA 0.000454 AA 2922.841797 916.889648
SNP_A-4265735 AA 0.006443 AA 2362.720703 536.849365
SNP_A-1995832 BB 0.003774 BB 582.085083 2524.016846
SNP_A-1995893 BB 0.003183 BB 578.443726 3500.974121
SNP_A-1997689 BB 0.001725 BB 777.788818 2827.456787
SNP_A-1997709 AA 0.003827 AA 976.906372 270.427979
SNP_A-1997896 AB 0.000126 AB 1526.090942 2100.442139
SNP_A-1997922 BB 0.006282 BB 578.333130 1125.004517
SNP_A-2000230 AB 0.001277 AB 1478.659424 1935.508057
SNP_A-2000332 AB 0.003110 AB 3237.095215 3269.779297
SNP_A-2000337 AB 0.001345 AB 1053.153198 1326.102539
SNP_A-2000342 AB 0.001480 AB 3037.013428 2919.865967
SNP_A-4268173 AB 0.006439 AB 1126.577637 1183.922119

Total number of rows: 909622

Table truncated, full table size 46153 Kbytes.




Supplementary file Size Download File type/resource
GSM731961_WX33-TL2.CEL.gz 29.5 Mb (ftp)(http) CEL
GSM731961_WX33-TL2.chp.gz 13.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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