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Status
Public on Feb 01, 2016
Title
blood-MTC_3569
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
0.001843
BB
996.333862
5279.784180
SNP_A-1967418
BB
0.016985
BB
315.956329
1015.893005
SNP_A-1969580
BB
0.002521
BB
1038.975342
4155.074219
SNP_A-4263484
BB
0.002290
BB
502.084076
1715.702393
SNP_A-1978185
AA
0.001492
AA
1412.765137
406.122620
SNP_A-4264431
AB
0.002240
AB
1285.766113
1080.585327
SNP_A-1980898
AB
0.002750
AB
690.133301
713.136841
SNP_A-1983139
AA
0.001319
AA
2766.615967
708.355225
SNP_A-4265735
AA
0.000920
AA
2058.421631
601.320435
SNP_A-1995832
AB
0.004836
AB
1920.430054
1543.295532
SNP_A-1995893
AB
0.004866
AB
1703.887939
1635.583984
SNP_A-1997689
BB
0.005495
BB
697.043518
2646.302002
SNP_A-1997709
AA
0.000383
AA
1777.817627
370.881561
SNP_A-1997896
AB
0.002350
AB
1137.273315
1515.832275
SNP_A-1997922
AA
0.001005
AA
832.026184
351.462555
SNP_A-2000230
AA
0.007355
AA
2549.512695
1014.886047
SNP_A-2000332
AB
0.018233
AB
3103.886475
3492.373291
SNP_A-2000337
AA
0.000298
AA
1383.349243
372.569519
SNP_A-2000342
AA
0.003200
AA
3670.059082
927.354431
SNP_A-4268173
AB
0.005559
AB
1211.405029
1095.668945
909622 46143 Kbytes .Supplementary file Size Download File type/resource GSM1636641_3569_GenomeWideSNP_6_.CEL.gz
28.9 Mb
(ftp) (http) CEL
GSM1636641_3569_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
