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Status
Public on Feb 01, 2016
Title
blood-MTC_1688R
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
0.075335
BB
1350.045532
3348.823242
SNP_A-1967418
AB
0.002730
AB
549.873657
481.729431
SNP_A-1969580
BB
0.009188
BB
1487.633057
4904.524414
SNP_A-4263484
BB
0.006329
BB
466.970856
1381.362671
SNP_A-1978185
AA
0.008087
AA
1633.755737
306.500702
SNP_A-4264431
AA
0.004656
AA
2254.212158
537.597717
SNP_A-1980898
BB
0.020276
BB
319.467377
1216.189331
SNP_A-1983139
AA
0.001949
AA
3110.761230
748.455933
SNP_A-4265735
AB
0.007826
AB
1706.821655
1315.982300
SNP_A-1995832
AA
0.004468
AA
2590.317139
844.505981
SNP_A-1995893
AA
0.002886
AA
2598.504395
1016.045471
SNP_A-1997689
BB
0.007123
BB
578.374146
2711.427734
SNP_A-1997709
AA
0.006022
AA
1253.030762
381.542511
SNP_A-1997896
AB
0.010734
AB
1391.803711
1667.069336
SNP_A-1997922
AA
0.027766
AA
460.482361
221.660126
SNP_A-2000230
AA
0.005131
AA
1986.604736
1295.182861
SNP_A-2000332
AB
0.011280
AB
3067.354248
3290.294922
SNP_A-2000337
AA
0.011783
AA
937.013977
404.761078
SNP_A-2000342
AA
0.003999
AA
2858.473877
911.067383
SNP_A-4268173
AA
0.014908
AA
2286.944824
381.542511
909622 46161 Kbytes .Supplementary file Size Download File type/resource GSM1636663_1688R_GenomeWideSNP_6_.CEL.gz
27.1 Mb
(ftp) (http) CEL
GSM1636663_1688R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
