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Status
Public on Feb 01, 2016
Title
blood-MTC_7660
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
0.007363
AB
2194.160156
2256.600830
SNP_A-1967418
NC
0.672629
AB
371.993011
478.914307
SNP_A-1969580
BB
0.001823
BB
1203.156738
4281.551270
SNP_A-4263484
BB
0.001504
BB
614.752563
1942.430664
SNP_A-1978185
AA
0.005170
AA
1977.667725
403.750977
SNP_A-4264431
AA
0.002202
AA
2007.606934
519.693542
SNP_A-1980898
BB
0.003861
BB
369.723724
832.583252
SNP_A-1983139
AA
0.002381
AA
3268.400879
911.265137
SNP_A-4265735
AA
0.007549
AA
1978.767334
860.678711
SNP_A-1995832
AB
0.001085
AB
1562.807007
1361.490845
SNP_A-1995893
AB
0.000732
AB
1599.416016
1762.635864
SNP_A-1997689
BB
0.005117
BB
648.338867
2785.737305
SNP_A-1997709
AA
0.004423
AA
1660.554688
289.182739
SNP_A-1997896
AA
0.008760
AA
1698.191895
706.668030
SNP_A-1997922
AB
0.034223
AB
386.591187
414.680023
SNP_A-2000230
AA
0.001751
AA
2250.024902
1141.378662
SNP_A-2000332
AA
0.004467
AA
4020.682373
957.194824
SNP_A-2000337
AA
0.013320
AA
904.404541
347.572205
SNP_A-2000342
AA
0.007142
AA
2904.873535
1139.490601
SNP_A-4268173
AB
0.010078
AB
1270.505859
1217.909668
909622 46159 Kbytes .Supplementary file Size Download File type/resource GSM1636608_7660_GenomeWideSNP_6_.CEL.gz
27.8 Mb
(ftp) (http) CEL
GSM1636608_7660_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
