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Sample GSM731974 Query DataSets for GSM731974
Status Public on Dec 31, 2011
Title WX76-TL2 prostate tumour
Sample type genomic
 
Source name WX76-TL2
Organism Homo sapiens
Characteristics tissue: WX76-TL2
individual: WX76
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 AB 0.001064 AB 1939.793701 2296.460693
SNP_A-1967418 BB 0.001160 BB 405.196716 1168.928467
SNP_A-1969580 BB 0.006077 BB 2172.655273 6468.128418
SNP_A-4263484 BB 0.001928 BB 627.759705 2253.971924
SNP_A-1978185 AA 0.002822 AA 1441.770508 365.860352
SNP_A-4264431 AA 0.003572 AA 3683.237305 714.392883
SNP_A-1980898 AB 0.004489 AB 1165.989624 994.043518
SNP_A-1983139 AA 0.001879 AA 2969.107422 1010.486572
SNP_A-4265735 AA 0.005044 AA 2510.486084 879.364319
SNP_A-1995832 BB 0.000693 BB 774.264893 2585.379883
SNP_A-1995893 BB 0.008721 BB 663.308899 2758.676025
SNP_A-1997689 BB 0.001848 BB 662.252380 2739.404541
SNP_A-1997709 AA 0.006085 AA 824.793091 314.240662
SNP_A-1997896 AB 0.011650 AB 2244.470215 2967.552734
SNP_A-1997922 AB 0.012301 AB 1151.735596 1013.247559
SNP_A-2000230 AA 0.004523 AA 1968.137939 737.461121
SNP_A-2000332 AA 0.001544 AA 4087.373291 823.478699
SNP_A-2000337 AA 0.001846 AA 1530.696289 361.277344
SNP_A-2000342 AA 0.001847 AA 4084.889648 1389.964355
SNP_A-4268173 AA 0.002772 AA 2288.080322 442.417999

Total number of rows: 909622

Table truncated, full table size 46172 Kbytes.




Supplementary file Size Download File type/resource
GSM731974_WX76-TL2.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM731974_WX76-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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