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Sample GSM1636613 Query DataSets for GSM1636613
Status Public on Feb 01, 2016
Title blood-MTC_6399
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 0.004816 BB 944.126404 3801.431641
SNP_A-1967418 BB 0.004979 BB 278.977112 770.255188
SNP_A-1969580 BB 0.001717 BB 1003.446228 3911.876709
SNP_A-4263484 AB 0.004026 AB 1334.311035 1139.247925
SNP_A-1978185 AA 0.001343 AA 1432.419189 408.196045
SNP_A-4264431 AB 0.000409 AB 1275.563965 973.418091
SNP_A-1980898 AB 0.001287 AB 774.763123 685.934265
SNP_A-1983139 AA 0.002448 AA 2743.152100 806.793640
SNP_A-4265735 AB 0.006061 AB 1305.574219 1075.097778
SNP_A-1995832 AB 0.001945 AB 1739.232666 1401.197510
SNP_A-1995893 AB 0.002659 AB 1606.254150 1649.763672
SNP_A-1997689 BB 0.003013 BB 848.572937 3109.568848
SNP_A-1997709 AA 0.003494 AA 2130.036133 352.217987
SNP_A-1997896 AA 0.003164 AA 1525.921753 591.307007
SNP_A-1997922 AB 0.015211 AB 475.345520 457.090576
SNP_A-2000230 AA 0.003816 AA 2189.717529 988.833557
SNP_A-2000332 AB 0.002316 AB 2358.733887 2780.700439
SNP_A-2000337 AA 0.002967 AA 1534.440063 425.616638
SNP_A-2000342 AA 0.004330 AA 2911.545654 822.981689
SNP_A-4268173 AA 0.006176 AA 1973.735962 347.418335

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM1636613_6399_GenomeWideSNP_6_.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM1636613_6399_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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