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Sample GSM1636638 Query DataSets for GSM1636638
Status Public on Feb 01, 2016
Title blood-MTC_3969
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 AA 0.001692 AA 5500.569336 822.538147
SNP_A-1967418 BB 0.003563 BB 372.426331 869.929749
SNP_A-1969580 BB 0.006685 BB 963.151550 4366.966797
SNP_A-4263484 AA 0.012493 AA 1925.354004 517.619263
SNP_A-1978185 AA 0.001675 AA 1403.379272 401.334259
SNP_A-4264431 AB 0.006806 AB 1366.748291 1237.435303
SNP_A-1980898 BB 0.003374 BB 363.848145 1033.982056
SNP_A-1983139 AA 0.010984 AA 1997.294312 558.694946
SNP_A-4265735 AB 0.001995 AB 1207.785034 1274.612061
SNP_A-1995832 AB 0.001419 AB 1683.072754 1387.944824
SNP_A-1995893 AB 0.000295 AB 1601.171875 1828.656006
SNP_A-1997689 BB 0.008991 BB 521.474304 2716.957520
SNP_A-1997709 AA 0.000180 AA 1794.524170 363.848145
SNP_A-1997896 AA 0.004507 AA 1551.024902 547.157776
SNP_A-1997922 AB 0.001151 AB 650.672607 594.063171
SNP_A-2000230 AA 0.011373 AA 2549.258057 853.623169
SNP_A-2000332 AA 0.024085 AA 4515.918457 692.338501
SNP_A-2000337 AA 0.006169 AA 1702.823242 354.499298
SNP_A-2000342 AA 0.002617 AA 3240.663086 814.113159
SNP_A-4268173 AA 0.004182 AA 1887.939575 349.221191

Total number of rows: 909622

Table truncated, full table size 46143 Kbytes.




Supplementary file Size Download File type/resource
GSM1636638_3969_GenomeWideSNP_6_.CEL.gz 28.5 Mb (ftp)(http) CEL
GSM1636638_3969_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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