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Sample GSM1637345 Query DataSets for GSM1637345
Status Public on Feb 01, 2016
Title blood-Control_6778
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: Control
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 0.001847 AB 2684.934326 2883.514648
SNP_A-1967418 BB 0.002071 BB 314.008423 787.113647
SNP_A-1969580 BB 0.001506 BB 1137.927368 4205.958496
SNP_A-4263484 AB 0.011930 AB 1825.316162 1011.396362
SNP_A-1978185 AA 0.001619 AA 1504.586060 480.232544
SNP_A-4264431 AB 0.003043 AB 1449.826660 1017.446716
SNP_A-1980898 AB 0.001416 AB 742.706909 618.386780
SNP_A-1983139 AA 0.002367 AA 2618.403564 687.662842
SNP_A-4265735 AA 0.001270 AA 2035.680298 579.697937
SNP_A-1995832 AB 0.002373 AB 1425.546143 1037.364990
SNP_A-1995893 AB 0.003567 AB 1383.269409 1774.653687
SNP_A-1997689 BB 0.003261 BB 864.601807 4325.658691
SNP_A-1997709 AA 0.005735 AA 1224.397339 265.302094
SNP_A-1997896 AB 0.004710 AB 1101.863770 1255.922852
SNP_A-1997922 AA 0.010285 AA 828.634460 416.296265
SNP_A-2000230 AA 0.004196 AA 2299.028564 1628.610352
SNP_A-2000332 AA 0.009199 AA 3459.449707 1293.587646
SNP_A-2000337 AA 0.009511 AA 1771.056885 442.760284
SNP_A-2000342 AA 0.007422 AA 3845.587646 1168.010742
SNP_A-4268173 AB 0.010882 AB 1065.621338 609.493225

Total number of rows: 909622

Table truncated, full table size 46156 Kbytes.




Supplementary file Size Download File type/resource
GSM1637345_6778_GenomeWideSNP_6_.CEL.gz 25.9 Mb (ftp)(http) CEL
GSM1637345_6778_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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