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Status
Public on Feb 01, 2016
Title
blood-MTC_2769
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
0.004396
BB
601.347961
4102.130859
SNP_A-1967418
BB
0.003913
BB
283.402863
730.485779
SNP_A-1969580
BB
0.005029
BB
1271.078979
4665.294434
SNP_A-4263484
AB
0.003374
AB
1351.322388
974.222229
SNP_A-1978185
AA
0.006637
AA
2152.015625
442.569458
SNP_A-4264431
AB
0.004156
AB
1377.842285
1161.088867
SNP_A-1980898
BB
0.002469
BB
387.164368
910.119019
SNP_A-1983139
AA
0.004993
AA
2427.076172
719.617676
SNP_A-4265735
AA
0.014081
AA
1039.712402
396.907257
SNP_A-1995832
AA
0.002870
AA
2036.549683
392.672272
SNP_A-1995893
AA
0.002057
AA
2524.009766
1004.534302
SNP_A-1997689
BB
0.005536
BB
588.743530
3711.533447
SNP_A-1997709
AA
0.003181
AA
2220.250000
414.318329
SNP_A-1997896
AA
0.010532
AA
1689.511963
502.631287
SNP_A-1997922
AA
0.011077
AA
1020.079956
298.506775
SNP_A-2000230
AA
0.004429
AA
2067.017334
964.791016
SNP_A-2000332
AA
0.004893
AA
3545.515381
759.479065
SNP_A-2000337
AA
0.000724
AA
1338.691040
377.689270
SNP_A-2000342
AA
0.010843
AA
4003.298340
764.334595
SNP_A-4268173
AA
0.000745
AA
1650.801025
342.343781
909622 46135 Kbytes .Supplementary file Size Download File type/resource GSM1636652_2769_GenomeWideSNP_6_.CEL.gz
29.1 Mb
(ftp) (http) CEL
GSM1636652_2769_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
