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Sample GSM1637405 Query DataSets for GSM1637405
Status Public on Feb 01, 2016
Title blood-Control_5486
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 0.000648 AB 2924.936523 2966.613525
SNP_A-1967418 BB 0.005173 BB 402.874176 762.871948
SNP_A-1969580 BB 0.002450 BB 1245.651001 3897.977051
SNP_A-4263484 BB 0.008547 BB 538.450317 2136.554443
SNP_A-1978185 AA 0.003333 AA 1392.247925 499.956299
SNP_A-4264431 AA 0.001393 AA 2015.992188 485.048676
SNP_A-1980898 AB 0.001967 AB 777.050720 628.177124
SNP_A-1983139 AA 0.001748 AA 2991.433594 713.319397
SNP_A-4265735 AA 0.002253 AA 2247.219238 617.918335
SNP_A-1995832 AB 0.001511 AB 1545.115967 1124.925537
SNP_A-1995893 AB 0.008767 AB 1202.825439 1613.008179
SNP_A-1997689 BB 0.001465 BB 727.421570 3708.527832
SNP_A-1997709 AA 0.002899 AA 1309.185913 317.883026
SNP_A-1997896 AA 0.001534 AA 1265.789795 531.772339
SNP_A-1997922 AB 0.001932 AB 592.066467 545.088440
SNP_A-2000230 AA 0.001336 AA 2385.105469 1403.767700
SNP_A-2000332 AA 0.001820 AA 3303.327148 887.993835
SNP_A-2000337 AA 0.010259 AA 1827.763306 389.579132
SNP_A-2000342 AA 0.000853 AA 3200.475830 925.875610
SNP_A-4268173 AB 0.003702 AB 1082.959351 769.971802

Total number of rows: 909622

Table truncated, full table size 46153 Kbytes.




Supplementary file Size Download File type/resource
GSM1637405_5486_GenomeWideSNP_6_.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM1637405_5486_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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