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Status
Public on Feb 01, 2016
Title
blood-MTC_2766
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
BB
0.002900
BB
832.108521
4086.022217
SNP_A-1967418
AB
0.004709
AB
523.236511
449.162903
SNP_A-1969580
BB
0.002384
BB
1082.704712
4231.055664
SNP_A-4263484
AB
0.003410
AB
1334.679321
1089.801270
SNP_A-1978185
AA
0.004523
AA
1915.058960
531.134094
SNP_A-4264431
AB
0.002234
AB
1363.784546
928.098694
SNP_A-1980898
BB
0.001584
BB
361.378052
983.871948
SNP_A-1983139
AA
0.002852
AA
2621.509766
753.970642
SNP_A-4265735
AB
0.010932
AB
950.249146
850.109619
SNP_A-1995832
AA
0.016554
AA
1641.969116
376.435974
SNP_A-1995893
AA
0.003350
AA
2616.686523
1009.210327
SNP_A-1997689
BB
0.003610
BB
672.963806
3940.050049
SNP_A-1997709
AA
0.002348
AA
1993.276733
412.341797
SNP_A-1997896
AA
0.004569
AA
1556.020874
549.499268
SNP_A-1997922
AA
0.010771
AA
940.571533
254.640945
SNP_A-2000230
AA
0.043400
AA
1708.852905
1206.788330
SNP_A-2000332
AA
0.000675
AA
3495.010742
1015.420654
SNP_A-2000337
AA
0.005231
AA
1263.387207
292.859039
SNP_A-2000342
AA
0.003727
AA
3564.808350
817.680176
SNP_A-4268173
AB
0.001392
AB
1075.614136
906.032166
909622 46133 Kbytes .Supplementary file Size Download File type/resource GSM1636653_2766_GenomeWideSNP_6_.CEL.gz
28.1 Mb
(ftp) (http) CEL
GSM1636653_2766_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
