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Status
Public on Feb 01, 2016
Title
blood-MTC_3034
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
0.005560
AB
3688.135986
3804.330322
SNP_A-1967418
BB
0.003804
BB
360.905060
880.359680
SNP_A-1969580
BB
0.006961
BB
1264.200562
4818.910156
SNP_A-4263484
AA
0.010591
AA
1872.030640
434.436646
SNP_A-1978185
AA
0.002396
AA
1342.242798
388.405762
SNP_A-4264431
AA
0.001754
AA
2035.958496
439.118469
SNP_A-1980898
AA
0.001933
AA
1225.862915
340.331146
SNP_A-1983139
AA
0.001067
AA
3087.493652
780.223022
SNP_A-4265735
AB
0.002852
AB
1162.157349
1201.036743
SNP_A-1995832
BB
0.039470
BB
427.455658
2868.074951
SNP_A-1995893
BB
0.004966
BB
617.119873
2280.557373
SNP_A-1997689
BB
0.009827
BB
583.535034
2329.568359
SNP_A-1997709
AA
0.002102
AA
1766.788330
324.825195
SNP_A-1997896
AB
0.001381
AB
1038.762085
1520.656128
SNP_A-1997922
AB
0.002166
AB
668.518372
577.506470
SNP_A-2000230
AA
0.020448
AA
2724.625244
754.320374
SNP_A-2000332
AA
0.031565
AA
5044.780762
958.332092
SNP_A-2000337
AA
0.006585
AA
1597.483643
291.962738
SNP_A-2000342
AA
0.004752
AA
3569.218750
774.439392
SNP_A-4268173
AA
0.004256
AA
1969.315796
410.803436
909622 46147 Kbytes .Supplementary file Size Download File type/resource GSM1636649_3034_GenomeWideSNP_6_.CEL.gz
27.2 Mb
(ftp) (http) CEL
GSM1636649_3034_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
