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Status
Public on Feb 01, 2016
Title
blood-MTC_6978
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
0.006663
AB
2330.121582
2239.702881
SNP_A-1967418
BB
0.000909
BB
338.241608
724.314270
SNP_A-1969580
BB
0.017038
BB
1713.050049
4753.582031
SNP_A-4263484
AB
0.006571
AB
1315.957520
837.547791
SNP_A-1978185
AA
0.004301
AA
1848.300781
386.821960
SNP_A-4264431
AA
0.002231
AA
2097.795898
494.088837
SNP_A-1980898
AA
0.002206
AA
1131.463501
310.449066
SNP_A-1983139
AA
0.003200
AA
3397.050537
894.368713
SNP_A-4265735
AA
0.000470
AA
1973.661011
629.386963
SNP_A-1995832
BB
0.000574
BB
734.086914
2026.055176
SNP_A-1995893
BB
0.002415
BB
624.528320
2521.482422
SNP_A-1997689
BB
0.007301
BB
690.939636
2438.831299
SNP_A-1997709
AA
0.004693
AA
1112.927612
309.511780
SNP_A-1997896
AB
0.008386
AB
1366.446167
1520.338989
SNP_A-1997922
AB
0.002563
AB
689.782654
629.296814
SNP_A-2000230
AA
0.004374
AA
1966.593750
1107.367065
SNP_A-2000332
AA
0.007369
AA
4255.974121
1048.883301
SNP_A-2000337
AA
0.003874
AA
1208.529663
332.239197
SNP_A-2000342
AA
0.001966
AA
3080.490234
1013.516907
SNP_A-4268173
AA
0.026322
AA
2661.780518
523.968933
909622 46160 Kbytes .Supplementary file Size Download File type/resource GSM1636612_6978_GenomeWideSNP_6_.CEL.gz
28.5 Mb
(ftp) (http) CEL
GSM1636612_6978_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
