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Status
Public on Feb 01, 2016
Title
blood-Control_5710
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
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
909622 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
