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Status
Public on Feb 01, 2016
Title
blood-MTC_7654
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
0.001238
AB
3167.537842
3310.339111
SNP_A-1967418
AB
0.008391
AB
696.715698
560.862000
SNP_A-1969580
BB
0.005187
BB
883.340149
3992.049316
SNP_A-4263484
AB
0.003457
AB
1326.808838
1068.342529
SNP_A-1978185
AA
0.002272
AA
1556.023438
383.826294
SNP_A-4264431
AA
0.009148
AA
2372.787598
425.408386
SNP_A-1980898
BB
0.003155
BB
317.164185
998.246338
SNP_A-1983139
AA
0.003776
AA
2612.147217
591.703979
SNP_A-4265735
AB
0.002263
AB
1293.942139
1240.323853
SNP_A-1995832
AB
0.007784
AB
1842.018066
1773.668823
SNP_A-1995893
AB
0.004870
AB
1832.968384
1999.357056
SNP_A-1997689
BB
0.003632
BB
640.802490
3177.579346
SNP_A-1997709
AA
0.004736
AA
2024.646240
320.171967
SNP_A-1997896
AA
0.008821
AA
1730.180176
634.134644
SNP_A-1997922
AB
0.008552
AB
448.794037
544.538025
SNP_A-2000230
AA
0.010611
AA
2205.621826
704.030945
SNP_A-2000332
AA
0.003848
AA
3717.486328
826.456909
SNP_A-2000337
AA
0.000495
AA
1356.217163
382.125427
SNP_A-2000342
AA
0.000445
AA
3242.078613
976.523621
SNP_A-4268173
AB
0.003488
AB
1187.013550
949.815674
909622 46139 Kbytes .Supplementary file Size Download File type/resource GSM1636609_7654_GenomeWideSNP_6_.CEL.gz
28.4 Mb
(ftp) (http) CEL
GSM1636609_7654_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
