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Status
Public on Feb 01, 2016
Title
blood-MTC_6399
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
0.004816
BB
944.126404
3801.431641
SNP_A-1967418
BB
0.004979
BB
278.977112
770.255188
SNP_A-1969580
BB
0.001717
BB
1003.446228
3911.876709
SNP_A-4263484
AB
0.004026
AB
1334.311035
1139.247925
SNP_A-1978185
AA
0.001343
AA
1432.419189
408.196045
SNP_A-4264431
AB
0.000409
AB
1275.563965
973.418091
SNP_A-1980898
AB
0.001287
AB
774.763123
685.934265
SNP_A-1983139
AA
0.002448
AA
2743.152100
806.793640
SNP_A-4265735
AB
0.006061
AB
1305.574219
1075.097778
SNP_A-1995832
AB
0.001945
AB
1739.232666
1401.197510
SNP_A-1995893
AB
0.002659
AB
1606.254150
1649.763672
SNP_A-1997689
BB
0.003013
BB
848.572937
3109.568848
SNP_A-1997709
AA
0.003494
AA
2130.036133
352.217987
SNP_A-1997896
AA
0.003164
AA
1525.921753
591.307007
SNP_A-1997922
AB
0.015211
AB
475.345520
457.090576
SNP_A-2000230
AA
0.003816
AA
2189.717529
988.833557
SNP_A-2000332
AB
0.002316
AB
2358.733887
2780.700439
SNP_A-2000337
AA
0.002967
AA
1534.440063
425.616638
SNP_A-2000342
AA
0.004330
AA
2911.545654
822.981689
SNP_A-4268173
AA
0.006176
AA
1973.735962
347.418335
909622 46139 Kbytes .Supplementary file Size Download File type/resource GSM1636613_6399_GenomeWideSNP_6_.CEL.gz
28.1 Mb
(ftp) (http) CEL
GSM1636613_6399_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
