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Status
Public on Feb 01, 2016
Title
blood-MTC_3867R
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
AB
0.001169
AB
3318.065186
3030.048340
SNP_A-1967418
BB
0.012798
BB
415.032654
713.099670
SNP_A-1969580
NC
0.582815
BB
1063.990845
2340.308105
SNP_A-4263484
AB
0.010171
AB
1945.692871
1237.758423
SNP_A-1978185
AB
0.010074
AB
1738.109619
1778.298340
SNP_A-4264431
AB
0.002387
AB
1096.124146
830.544861
SNP_A-1980898
AB
0.004011
AB
699.568970
555.299377
SNP_A-1983139
AA
0.004310
AA
3153.376709
980.444336
SNP_A-4265735
AA
0.004799
AA
1926.729614
783.039429
SNP_A-1995832
AB
0.002896
AB
1709.841431
1168.457764
SNP_A-1995893
AB
0.012042
AB
1304.093018
2031.779541
SNP_A-1997689
BB
0.017008
BB
1220.242798
3792.389893
SNP_A-1997709
AA
0.007274
AA
2083.275635
471.029663
SNP_A-1997896
AB
0.000373
AB
998.398987
1461.140381
SNP_A-1997922
AA
0.001597
AA
832.664978
365.213928
SNP_A-2000230
AB
0.001865
AB
1622.142212
2467.746826
SNP_A-2000332
AB
0.003228
AB
2288.263184
2519.136963
SNP_A-2000337
AA
0.078780
AA
1007.265869
583.234131
SNP_A-2000342
NC
0.139254
AA
2987.910645
1404.174683
SNP_A-4268173
AB
0.001541
AB
864.205872
795.813354
909622 46148 Kbytes .Supplementary file Size Download File type/resource GSM1636639_3867R_GenomeWideSNP_6_.CEL.gz
29.2 Mb
(ftp) (http) CEL
GSM1636639_3867R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
