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Sample GSM1636649 Query DataSets for GSM1636649
Status Public on Feb 01, 2016
Title blood-MTC_3034
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 0.005560 AB 3688.135986 3804.330322
SNP_A-1967418 BB 0.003804 BB 360.905060 880.359680
SNP_A-1969580 BB 0.006961 BB 1264.200562 4818.910156
SNP_A-4263484 AA 0.010591 AA 1872.030640 434.436646
SNP_A-1978185 AA 0.002396 AA 1342.242798 388.405762
SNP_A-4264431 AA 0.001754 AA 2035.958496 439.118469
SNP_A-1980898 AA 0.001933 AA 1225.862915 340.331146
SNP_A-1983139 AA 0.001067 AA 3087.493652 780.223022
SNP_A-4265735 AB 0.002852 AB 1162.157349 1201.036743
SNP_A-1995832 BB 0.039470 BB 427.455658 2868.074951
SNP_A-1995893 BB 0.004966 BB 617.119873 2280.557373
SNP_A-1997689 BB 0.009827 BB 583.535034 2329.568359
SNP_A-1997709 AA 0.002102 AA 1766.788330 324.825195
SNP_A-1997896 AB 0.001381 AB 1038.762085 1520.656128
SNP_A-1997922 AB 0.002166 AB 668.518372 577.506470
SNP_A-2000230 AA 0.020448 AA 2724.625244 754.320374
SNP_A-2000332 AA 0.031565 AA 5044.780762 958.332092
SNP_A-2000337 AA 0.006585 AA 1597.483643 291.962738
SNP_A-2000342 AA 0.004752 AA 3569.218750 774.439392
SNP_A-4268173 AA 0.004256 AA 1969.315796 410.803436

Total number of rows: 909622

Table truncated, full table size 46147 Kbytes.




Supplementary file Size Download File type/resource
GSM1636649_3034_GenomeWideSNP_6_.CEL.gz 27.2 Mb (ftp)(http) CEL
GSM1636649_3034_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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