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Status
Public on Feb 01, 2016
Title
blood-MTC_3969
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens Characteristics
phenotype: MTC
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
AA
0.001692
AA
5500.569336
822.538147
SNP_A-1967418
BB
0.003563
BB
372.426331
869.929749
SNP_A-1969580
BB
0.006685
BB
963.151550
4366.966797
SNP_A-4263484
AA
0.012493
AA
1925.354004
517.619263
SNP_A-1978185
AA
0.001675
AA
1403.379272
401.334259
SNP_A-4264431
AB
0.006806
AB
1366.748291
1237.435303
SNP_A-1980898
BB
0.003374
BB
363.848145
1033.982056
SNP_A-1983139
AA
0.010984
AA
1997.294312
558.694946
SNP_A-4265735
AB
0.001995
AB
1207.785034
1274.612061
SNP_A-1995832
AB
0.001419
AB
1683.072754
1387.944824
SNP_A-1995893
AB
0.000295
AB
1601.171875
1828.656006
SNP_A-1997689
BB
0.008991
BB
521.474304
2716.957520
SNP_A-1997709
AA
0.000180
AA
1794.524170
363.848145
SNP_A-1997896
AA
0.004507
AA
1551.024902
547.157776
SNP_A-1997922
AB
0.001151
AB
650.672607
594.063171
SNP_A-2000230
AA
0.011373
AA
2549.258057
853.623169
SNP_A-2000332
AA
0.024085
AA
4515.918457
692.338501
SNP_A-2000337
AA
0.006169
AA
1702.823242
354.499298
SNP_A-2000342
AA
0.002617
AA
3240.663086
814.113159
SNP_A-4268173
AA
0.004182
AA
1887.939575
349.221191
909622 46143 Kbytes .Supplementary file Size Download File type/resource GSM1636638_3969_GenomeWideSNP_6_.CEL.gz
28.5 Mb
(ftp) (http) CEL
GSM1636638_3969_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
