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Sample GSM1636633 Query DataSets for GSM1636633
Status Public on Feb 01, 2016
Title blood-MTC_4267R
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 0.010984 AA 4335.460449 1442.714966
SNP_A-1967418 BB 0.010526 BB 427.923187 951.545288
SNP_A-1969580 BB 0.007138 BB 992.448853 3093.990723
SNP_A-4263484 BB 0.014394 BB 888.774597 2363.353027
SNP_A-1978185 AA 0.024286 AA 2584.858154 652.268066
SNP_A-4264431 AB 0.000586 AB 1241.621582 920.826294
SNP_A-1980898 AB 0.006613 AB 723.641602 516.678284
SNP_A-1983139 AA 0.058623 AA 3118.450439 1443.441650
SNP_A-4265735 AA 0.004413 AA 2022.967896 804.699158
SNP_A-1995832 BB 0.001612 BB 825.691467 1909.596802
SNP_A-1995893 BB 0.022735 BB 833.823853 3219.772705
SNP_A-1997689 BB 0.019593 BB 1262.449829 4386.042480
SNP_A-1997709 AA 0.007189 AA 1492.450806 425.779022
SNP_A-1997896 AB 0.004323 AB 1139.131836 1636.062744
SNP_A-1997922 AB 0.006089 AB 673.506348 702.613525
SNP_A-2000230 AA 0.032820 AA 2206.325195 1899.670410
SNP_A-2000332 BB 0.029301 BB 1656.245483 3298.933350
SNP_A-2000337 AA 0.006035 AA 1174.763916 453.619476
SNP_A-2000342 NC 0.160193 AA 2947.890137 1403.266968
SNP_A-4268173 AA 0.008325 AA 1460.741089 478.282440

Total number of rows: 909622

Table truncated, full table size 46137 Kbytes.




Supplementary file Size Download File type/resource
GSM1636633_4267R_GenomeWideSNP_6_.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM1636633_4267R_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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