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Status
Public on Feb 01, 2016
Title
blood-MTC_5877
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
0.006025
AB
4014.842285
3254.704834
SNP_A-1967418
BB
0.001269
BB
348.519928
724.348450
SNP_A-1969580
BB
0.008875
BB
718.189392
3120.689941
SNP_A-4263484
BB
0.000527
BB
607.273804
1781.833130
SNP_A-1978185
AA
0.006132
AA
2131.424561
448.855560
SNP_A-4264431
AA
0.005893
AA
2034.229248
336.014343
SNP_A-1980898
BB
0.001457
BB
375.224152
950.722778
SNP_A-1983139
AA
0.004409
AA
2760.027100
878.476501
SNP_A-4265735
BB
0.001691
BB
697.510742
1810.139771
SNP_A-1995832
AA
0.002849
AA
2357.600830
425.040985
SNP_A-1995893
AA
0.001635
AA
2557.781006
1049.702148
SNP_A-1997689
BB
0.001876
BB
778.148499
3186.400391
SNP_A-1997709
AA
0.003986
AA
2312.300537
389.430115
SNP_A-1997896
AA
0.002402
AA
1354.739624
510.484406
SNP_A-1997922
AA
0.008581
AA
959.834778
284.063232
SNP_A-2000230
AA
0.024004
AA
3182.921875
1412.375854
SNP_A-2000332
AB
0.003442
AB
2847.937988
2961.225098
SNP_A-2000337
AA
0.002821
AA
1213.222046
379.340057
SNP_A-2000342
AA
0.006094
AA
3880.639160
905.620728
SNP_A-4268173
AA
0.001063
AA
1458.569580
320.382843
909622 46146 Kbytes .Supplementary file Size Download File type/resource GSM1636618_5877_GenomeWideSNP_6_.CEL.gz
28.0 Mb
(ftp) (http) CEL
GSM1636618_5877_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
