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Status
Public on Feb 01, 2016
Title
blood-MTC_3550R
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
AA
0.010745
AA
4043.631348
1243.822998
SNP_A-1967418
BB
0.001053
BB
328.743866
783.713928
SNP_A-1969580
BB
0.016953
BB
1564.697388
4048.989014
SNP_A-4263484
BB
0.001542
BB
612.901489
1943.679077
SNP_A-1978185
AB
0.010017
AB
1249.970703
1200.322266
SNP_A-4264431
AB
0.001850
AB
1208.896362
849.014282
SNP_A-1980898
BB
0.000445
BB
348.933594
911.145325
SNP_A-1983139
AA
0.007715
AA
3328.498047
1083.222168
SNP_A-4265735
AA
0.003879
AA
1824.919678
717.384644
SNP_A-1995832
AA
0.007185
AA
2869.496094
671.638977
SNP_A-1995893
AA
0.004478
AA
2423.367188
1258.002197
SNP_A-1997689
BB
0.003955
BB
944.946106
3375.495117
SNP_A-1997709
AA
0.037193
AA
3189.146484
619.231506
SNP_A-1997896
AA
0.002160
AA
1426.666016
654.104736
SNP_A-1997922
AA
0.012357
AA
599.223328
287.118988
SNP_A-2000230
AA
0.001035
AA
2162.045898
1251.751587
SNP_A-2000332
AA
0.002736
AA
3146.306641
975.651245
SNP_A-2000337
AA
0.007062
AA
1673.499634
452.852722
SNP_A-2000342
AA
0.008889
AA
2945.643555
1182.502563
SNP_A-4268173
AB
0.003930
AB
990.689514
691.642944
909622 46140 Kbytes .Supplementary file Size Download File type/resource GSM1636642_3550R_GenomeWideSNP_6_.CEL.gz
29.8 Mb
(ftp) (http) CEL
GSM1636642_3550R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.2 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
