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Sample GSM1636639 Query DataSets for GSM1636639
Status Public on Feb 01, 2016
Title blood-MTC_3867R
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 0.001169 AB 3318.065186 3030.048340
SNP_A-1967418 BB 0.012798 BB 415.032654 713.099670
SNP_A-1969580 NC 0.582815 BB 1063.990845 2340.308105
SNP_A-4263484 AB 0.010171 AB 1945.692871 1237.758423
SNP_A-1978185 AB 0.010074 AB 1738.109619 1778.298340
SNP_A-4264431 AB 0.002387 AB 1096.124146 830.544861
SNP_A-1980898 AB 0.004011 AB 699.568970 555.299377
SNP_A-1983139 AA 0.004310 AA 3153.376709 980.444336
SNP_A-4265735 AA 0.004799 AA 1926.729614 783.039429
SNP_A-1995832 AB 0.002896 AB 1709.841431 1168.457764
SNP_A-1995893 AB 0.012042 AB 1304.093018 2031.779541
SNP_A-1997689 BB 0.017008 BB 1220.242798 3792.389893
SNP_A-1997709 AA 0.007274 AA 2083.275635 471.029663
SNP_A-1997896 AB 0.000373 AB 998.398987 1461.140381
SNP_A-1997922 AA 0.001597 AA 832.664978 365.213928
SNP_A-2000230 AB 0.001865 AB 1622.142212 2467.746826
SNP_A-2000332 AB 0.003228 AB 2288.263184 2519.136963
SNP_A-2000337 AA 0.078780 AA 1007.265869 583.234131
SNP_A-2000342 NC 0.139254 AA 2987.910645 1404.174683
SNP_A-4268173 AB 0.001541 AB 864.205872 795.813354

Total number of rows: 909622

Table truncated, full table size 46148 Kbytes.




Supplementary file Size Download File type/resource
GSM1636639_3867R_GenomeWideSNP_6_.CEL.gz 29.2 Mb (ftp)(http) CEL
GSM1636639_3867R_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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