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Status
Public on Feb 01, 2016
Title
blood-MTC_7311
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
0.008258
AB
2153.153076
2178.826904
SNP_A-1967418
BB
0.008604
BB
390.931610
687.739868
SNP_A-1969580
BB
0.018609
BB
1740.792847
4845.178711
SNP_A-4263484
BB
0.008980
BB
464.128296
1278.667969
SNP_A-1978185
AA
0.006970
AA
2049.127930
390.402679
SNP_A-4264431
AB
0.002132
AB
1399.482300
1026.108154
SNP_A-1980898
AB
0.012364
AB
850.616394
862.448181
SNP_A-1983139
AA
0.021714
AA
3180.820068
1236.350220
SNP_A-4265735
AB
0.000854
AB
1499.871948
1468.898804
SNP_A-1995832
AA
0.001000
AA
2429.994629
626.534363
SNP_A-1995893
AA
0.014205
AA
3053.533691
1117.372437
SNP_A-1997689
BB
0.014842
BB
570.721924
1916.399292
SNP_A-1997709
AA
0.003675
AA
1353.641724
291.152161
SNP_A-1997896
AA
0.003654
AA
1543.903198
643.276428
SNP_A-1997922
AA
0.036909
AA
605.155884
336.853821
SNP_A-2000230
AA
0.003886
AA
2447.363525
1116.307373
SNP_A-2000332
AB
0.015203
AB
3312.201416
3285.838623
SNP_A-2000337
AA
0.004758
AA
1135.541870
398.152222
SNP_A-2000342
AA
0.011462
AA
2815.894775
1173.312012
SNP_A-4268173
AB
0.022133
AB
1545.501465
967.055603
909622 46157 Kbytes .Supplementary file Size Download File type/resource GSM1636611_7311_GenomeWideSNP_6_.CEL.gz
28.1 Mb
(ftp) (http) CEL
GSM1636611_7311_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
