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Status
Public on Feb 01, 2016
Title
blood-Control_1504
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens Characteristics
phenotype: Control
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 Yúfera, 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
0.021126
AB
4075.318604
4753.173340
SNP_A-1967418
BB
0.005676
BB
350.522949
914.834961
SNP_A-1969580
BB
0.008517
BB
1492.873657
4182.407715
SNP_A-4263484
BB
0.006730
BB
619.990112
1481.822876
SNP_A-1978185
AA
0.015761
AA
826.941467
531.649780
SNP_A-4264431
AA
0.002314
AA
1671.637207
435.399872
SNP_A-1980898
AB
0.002694
AB
697.204651
583.434326
SNP_A-1983139
AA
0.005228
AA
3550.483887
885.098755
SNP_A-4265735
AB
0.015809
AB
2194.523438
2154.324707
SNP_A-1995832
AB
0.013394
AB
2200.742432
1840.581665
SNP_A-1995893
AB
0.012515
AB
1919.563110
2306.062988
SNP_A-1997689
BB
0.005056
BB
651.138733
2788.093994
SNP_A-1997709
AA
0.002977
AA
2194.024902
412.598541
SNP_A-1997896
AB
0.008630
AB
814.002808
1104.880127
SNP_A-1997922
AA
0.009995
AA
652.058350
318.872742
SNP_A-2000230
AA
0.001190
AA
2148.020020
1251.767456
SNP_A-2000332
AA
0.002583
AA
3586.215576
847.242981
SNP_A-2000337
AA
0.001705
AA
1517.806885
377.398560
SNP_A-2000342
AA
0.003983
AA
3008.623535
1089.208008
SNP_A-4268173
AA
0.002684
AA
1427.694580
372.026184
909622 46134 Kbytes .Supplementary file Size Download File type/resource GSM1637459_1504_GenomeWideSNP_6_.CEL.gz
29.5 Mb
(ftp) (http) CEL
GSM1637459_1504_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
