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Sample GSM1637394 Query DataSets for GSM1637394
Status Public on Feb 01, 2016
Title blood-Control_5710
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 BB 0.016550 BB 1774.434204 4555.635254
SNP_A-1967418 BB 0.005323 BB 301.021545 847.996948
SNP_A-1969580 BB 0.000884 BB 1121.911865 3808.283691
SNP_A-4263484 AB 0.004554 AB 1277.518433 983.267578
SNP_A-1978185 AA 0.004740 AA 1147.754395 466.862000
SNP_A-4264431 AA 0.009108 AA 1680.507812 568.193726
SNP_A-1980898 BB 0.016060 BB 359.665771 688.012573
SNP_A-1983139 AA 0.001762 AA 2702.151611 737.580811
SNP_A-4265735 AB 0.004949 AB 1672.550537 1832.988525
SNP_A-1995832 AA 0.047227 AA 2435.076660 1121.279419
SNP_A-1995893 AA 0.007554 AA 2006.609985 992.826416
SNP_A-1997689 BB 0.012608 BB 1155.567749 3667.104980
SNP_A-1997709 AA 0.002691 AA 1335.109497 319.754456
SNP_A-1997896 AA 0.009129 AA 1147.754395 740.088562
SNP_A-1997922 AA 0.004158 AA 924.320129 393.077942
SNP_A-2000230 AA 0.009283 AA 2146.036865 1644.888916
SNP_A-2000332 AA 0.009880 AA 3170.360596 1255.506104
SNP_A-2000337 AA 0.002769 AA 1558.824707 407.807404
SNP_A-2000342 NC 0.229655 AA 3116.331543 1456.827759
SNP_A-4268173 AB 0.003098 AB 837.824097 665.933716

Total number of rows: 909622

Table truncated, full table size 46164 Kbytes.




Supplementary file Size Download File type/resource
GSM1637394_5710_GenomeWideSNP_6_.CEL.gz 26.5 Mb (ftp)(http) CEL
GSM1637394_5710_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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