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Sample GSM1636603 Query DataSets for GSM1636603
Status Public on Feb 01, 2016
Title blood-MTC_9480
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: MTC
tissue: peripheral blood
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from peripheral blood using MagNA Pure LC 2.0 System. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
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 images were obtained using an Affymetrix GeneChip® Scanner 3000.
Data processing CEL files were processed using Affymetrix Power Tools (APT v1.15.0) using Birdseed v2 calling algorithm.
 
Submission date Mar 18, 2015
Last update date Feb 01, 2016
Contact name Joaquin Dopazo
E-mail(s) jdopazo@cipf.es
Organization name Centro de Investigacion Principe Felipe
Department Systems Biology
Street address Eduardo Primo Y├║fera, 3
City Valencia
State/province Valencia
ZIP/Postal code 46012
Country Spain
 
Platform ID GPL6801
Series (1)
GSE67047 Genome-wide association and epistatic studies in sporadic medullary and juvenile papillary thyroid carcinomas

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
CONFIDENCE
FORCED CALL
SIGNAL A Summarized signal
SIGNAL B Summarized signal

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.001656 BB 1036.860718 5259.680664
SNP_A-1967418 BB 0.002160 BB 325.995453 816.326843
SNP_A-1969580 BB 0.002975 BB 924.402954 3790.225098
SNP_A-4263484 AB 0.005184 AB 1270.217041 925.950317
SNP_A-1978185 AA 0.001811 AA 1331.456177 430.671967
SNP_A-4264431 AB 0.004132 AB 1443.419556 1147.468506
SNP_A-1980898 AB 0.004274 AB 715.441833 551.047302
SNP_A-1983139 AA 0.006566 AA 2593.602783 508.974915
SNP_A-4265735 AA 0.004553 AA 1567.327515 595.388245
SNP_A-1995832 AB 0.002982 AB 1787.961060 1495.105225
SNP_A-1995893 AB 0.007909 AB 1866.688721 1740.145508
SNP_A-1997689 BB 0.008096 BB 512.410645 3366.454102
SNP_A-1997709 AA 0.001410 AA 1597.857056 327.926147
SNP_A-1997896 AA 0.005543 AA 1626.990356 608.497986
SNP_A-1997922 AB 0.005352 AB 484.761414 539.339050
SNP_A-2000230 AA 0.007947 AA 1888.656982 865.740540
SNP_A-2000332 AB 0.002132 AB 2833.109375 2760.402832
SNP_A-2000337 AA 0.003106 AA 1565.832153 347.498260
SNP_A-2000342 AA 0.005314 AA 3514.660156 739.236450
SNP_A-4268173 AB 0.001754 AB 998.006409 770.653625

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.




Supplementary file Size Download File type/resource
GSM1636603_9480_GenomeWideSNP_6_.CEL.gz 27.6 Mb (ftp)(http) CEL
GSM1636603_9480_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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