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Sample GSM1636612 Query DataSets for GSM1636612
Status Public on Feb 01, 2016
Title blood-MTC_6978
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 AB 0.006663 AB 2330.121582 2239.702881
SNP_A-1967418 BB 0.000909 BB 338.241608 724.314270
SNP_A-1969580 BB 0.017038 BB 1713.050049 4753.582031
SNP_A-4263484 AB 0.006571 AB 1315.957520 837.547791
SNP_A-1978185 AA 0.004301 AA 1848.300781 386.821960
SNP_A-4264431 AA 0.002231 AA 2097.795898 494.088837
SNP_A-1980898 AA 0.002206 AA 1131.463501 310.449066
SNP_A-1983139 AA 0.003200 AA 3397.050537 894.368713
SNP_A-4265735 AA 0.000470 AA 1973.661011 629.386963
SNP_A-1995832 BB 0.000574 BB 734.086914 2026.055176
SNP_A-1995893 BB 0.002415 BB 624.528320 2521.482422
SNP_A-1997689 BB 0.007301 BB 690.939636 2438.831299
SNP_A-1997709 AA 0.004693 AA 1112.927612 309.511780
SNP_A-1997896 AB 0.008386 AB 1366.446167 1520.338989
SNP_A-1997922 AB 0.002563 AB 689.782654 629.296814
SNP_A-2000230 AA 0.004374 AA 1966.593750 1107.367065
SNP_A-2000332 AA 0.007369 AA 4255.974121 1048.883301
SNP_A-2000337 AA 0.003874 AA 1208.529663 332.239197
SNP_A-2000342 AA 0.001966 AA 3080.490234 1013.516907
SNP_A-4268173 AA 0.026322 AA 2661.780518 523.968933

Total number of rows: 909622

Table truncated, full table size 46160 Kbytes.




Supplementary file Size Download File type/resource
GSM1636612_6978_GenomeWideSNP_6_.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM1636612_6978_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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