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Sample GSM1636662 Query DataSets for GSM1636662
Status Public on Feb 01, 2016
Title blood-MTC_2114
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 0.005139 BB 515.546265 4601.450684
SNP_A-1967418 BB 0.001043 BB 331.344330 788.405334
SNP_A-1969580 BB 0.004846 BB 944.393250 4159.850586
SNP_A-4263484 AB 0.003762 AB 1350.911743 1151.463257
SNP_A-1978185 AA 0.041822 AA 3059.926270 643.051514
SNP_A-4264431 AA 0.018094 AA 2298.339355 282.692566
SNP_A-1980898 AB 0.006215 AB 857.483215 618.548035
SNP_A-1983139 AA 0.006137 AA 2838.582275 555.532837
SNP_A-4265735 AA 0.005620 AA 1552.518433 375.804718
SNP_A-1995832 AB 0.023442 AB 848.821350 839.449402
SNP_A-1995893 AB 0.006329 AB 1550.318604 1473.714478
SNP_A-1997689 BB 0.006596 BB 563.667480 3724.015137
SNP_A-1997709 AA 0.013537 AA 1870.932373 498.829865
SNP_A-1997896 AA 0.005915 AA 1423.469727 451.354584
SNP_A-1997922 AB 0.001697 AB 649.396729 571.375732
SNP_A-2000230 AA 0.007453 AA 2306.785400 847.461182
SNP_A-2000332 AB 0.004374 AB 2969.708252 2640.961670
SNP_A-2000337 AA 0.011259 AA 1448.084473 226.074982
SNP_A-2000342 AA 0.011734 AA 3631.432617 596.570740
SNP_A-4268173 AA 0.004246 AA 1353.154053 377.902863

Total number of rows: 909622

Table truncated, full table size 46133 Kbytes.




Supplementary file Size Download File type/resource
GSM1636662_2114_GenomeWideSNP_6_.CEL.gz 26.6 Mb (ftp)(http) CEL
GSM1636662_2114_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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