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Sample GSM775361 Query DataSets for GSM775361
Status Public on Dec 31, 2011
Title P123-TL1 prostate tumour
Sample type genomic
 
Source name P123-TL
Organism Homo sapiens
Characteristics individual: P123
tissue: Prostate tissue
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 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 Aug 09, 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 0.001209 BB 972.569824 3470.357178
SNP_A-1967418 BB 0.002499 BB 305.609009 1052.645020
SNP_A-1969580 BB 0.005702 BB 1256.648560 4917.054688
SNP_A-4263484 BB 0.004531 BB 435.335968 1751.042236
SNP_A-1978185 AA 0.003259 AA 1413.922119 279.297241
SNP_A-4264431 AB 0.005236 AB 1638.652344 1137.723267
SNP_A-1980898 BB 0.003391 BB 288.930237 1279.628418
SNP_A-1983139 AA 0.002903 AA 2665.697998 744.030518
SNP_A-4265735 AA 0.002304 AA 2461.548828 727.854065
SNP_A-1995832 BB 0.001634 BB 833.438354 2474.482910
SNP_A-1995893 BB 0.001488 BB 600.204712 3396.473389
SNP_A-1997689 BB 0.014379 BB 980.297180 4306.104004
SNP_A-1997709 AA 0.002743 AA 1129.813232 265.891754
SNP_A-1997896 AB 0.003079 AB 1298.964355 1635.481445
SNP_A-1997922 AB 0.002641 AB 881.606018 741.019592
SNP_A-2000230 AA 0.004934 AA 2501.775879 1256.543213
SNP_A-2000332 AA 0.001084 AA 4189.202148 870.814392
SNP_A-2000337 AA 0.001440 AA 1603.679810 415.992432
SNP_A-2000342 AA 0.003611 AA 4197.313477 1107.434814
SNP_A-4268173 AA 0.002203 AA 1766.355591 381.730682

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.




Supplementary file Size Download File type/resource
GSM775361_P123-TL1.CEL.gz 28.8 Mb (ftp)(http) CEL
GSM775361_P123-TL1.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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