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Status
Public on Feb 01, 2016
Title
blood-MTC_3122
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
0.004834
BB
741.864502
3782.777100
SNP_A-1967418
AB
0.009973
AB
732.687439
654.932129
SNP_A-1969580
BB
0.004173
BB
1059.925537
4369.975586
SNP_A-4263484
AB
0.008280
AB
1359.630859
790.606018
SNP_A-1978185
AA
0.001640
AA
1785.223022
453.304260
SNP_A-4264431
AB
0.001331
AB
1346.313843
1008.238953
SNP_A-1980898
AA
0.005641
AA
1234.513062
281.545563
SNP_A-1983139
AA
0.002013
AA
2767.078613
799.547729
SNP_A-4265735
AB
0.018244
AB
777.594910
735.838440
SNP_A-1995832
BB
0.008804
BB
354.193512
1769.172363
SNP_A-1995893
BB
0.004581
BB
564.149719
2198.902100
SNP_A-1997689
BB
0.007640
BB
521.700684
3338.639160
SNP_A-1997709
AA
0.014013
AA
2336.855713
290.718903
SNP_A-1997896
BB
0.001832
BB
521.700684
2192.901123
SNP_A-1997922
AA
0.001763
AA
761.664673
336.732483
SNP_A-2000230
AA
0.018782
AA
1666.937622
846.494873
SNP_A-2000332
AB
0.001904
AB
2608.688721
2537.322998
SNP_A-2000337
AA
0.005079
AA
1369.594360
284.874664
SNP_A-2000342
AA
0.028392
AA
2783.571289
361.389679
SNP_A-4268173
AA
0.002073
AA
1413.299805
266.763428
909622 46133 Kbytes .Supplementary file Size Download File type/resource GSM1636648_3122_GenomeWideSNP_6_.CEL.gz
25.5 Mb
(ftp) (http) CEL
GSM1636648_3122_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
