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Sample GSM1636643 Query DataSets for GSM1636643
Status Public on Feb 01, 2016
Title blood-MTC_3356R
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 0.004200 BB 1106.007446 4037.048340
SNP_A-1967418 BB 0.005987 BB 386.527710 701.742126
SNP_A-1969580 BB 0.006176 BB 962.500000 3139.569824
SNP_A-4263484 AB 0.001746 AB 1670.067993 1227.116821
SNP_A-1978185 AA 0.008531 AA 2068.469971 578.965454
SNP_A-4264431 AA 0.016568 AA 1384.526367 466.159058
SNP_A-1980898 BB 0.003837 BB 329.503601 808.432312
SNP_A-1983139 AA 0.001460 AA 2791.688965 784.318848
SNP_A-4265735 AA 0.007784 AA 2057.162598 889.170715
SNP_A-1995832 BB 0.002088 BB 868.742371 2212.724854
SNP_A-1995893 BB 0.003401 BB 652.926086 2616.828857
SNP_A-1997689 BB 0.009964 BB 1122.406250 3873.437988
SNP_A-1997709 AA 0.002775 AA 1560.886108 387.305573
SNP_A-1997896 AB 0.004418 AB 1226.183105 1558.965454
SNP_A-1997922 AB 0.002044 AB 677.294067 620.558594
SNP_A-2000230 AA 0.012194 AA 2015.016235 1510.173462
SNP_A-2000332 AB 0.005319 AB 2397.018799 2315.933105
SNP_A-2000337 AA 0.013994 AA 955.985474 464.246033
SNP_A-2000342 AA 0.004616 AA 2977.785889 1099.797241
SNP_A-4268173 AA 0.016533 AA 1274.242188 473.565521

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.




Supplementary file Size Download File type/resource
GSM1636643_3356R_GenomeWideSNP_6_.CEL.gz 29.6 Mb (ftp)(http) CEL
GSM1636643_3356R_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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