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Status
Public on Feb 01, 2016
Title
blood-MTC_4354
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
0.001178
AB
2958.337646
3226.968262
SNP_A-1967418
BB
0.037920
BB
357.674835
568.735352
SNP_A-1969580
BB
0.001881
BB
1004.540771
3622.151611
SNP_A-4263484
BB
0.001733
BB
524.024231
1670.027222
SNP_A-1978185
AA
0.002013
AA
1729.972534
493.822540
SNP_A-4264431
AA
0.004325
AA
1514.445679
360.233154
SNP_A-1980898
BB
0.007489
BB
418.634460
843.596680
SNP_A-1983139
AA
0.009142
AA
3718.844238
855.109558
SNP_A-4265735
AB
0.001209
AB
1303.066284
1322.267212
SNP_A-1995832
AB
0.008074
AB
1047.131348
945.571777
SNP_A-1995893
AB
0.005102
AB
1670.027222
2114.090332
SNP_A-1997689
BB
0.006534
BB
619.452820
4149.113281
SNP_A-1997709
AA
0.003567
AA
2176.515869
360.233154
SNP_A-1997896
AA
0.010845
AA
1490.071533
398.530640
SNP_A-1997922
AB
0.007359
AB
509.646515
605.705688
SNP_A-2000230
AA
0.003120
AA
2067.955322
1068.106445
SNP_A-2000332
AA
0.001534
AA
3558.188477
1066.014404
SNP_A-2000337
AA
0.002844
AA
1404.996216
317.358826
SNP_A-2000342
AA
0.001883
AA
3509.218262
906.042358
SNP_A-4268173
AA
0.001196
AA
1589.218384
385.731750
909622 46144 Kbytes .Supplementary file Size Download File type/resource GSM1636632_4354_GenomeWideSNP_6_.CEL.gz
26.7 Mb
(ftp) (http) CEL
GSM1636632_4354_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
