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Status
Public on Feb 01, 2016
Title
blood-PTC_E14181
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens Characteristics
phenotype: PTC
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
AA
0.007091
AA
4049.926270
736.653992
SNP_A-1967418
BB
0.003158
BB
367.529449
724.498596
SNP_A-1969580
BB
0.007877
BB
697.653320
2767.619629
SNP_A-4263484
AB
0.004396
AB
1600.447144
1412.850708
SNP_A-1978185
AA
0.005684
AA
2006.388916
540.259705
SNP_A-4264431
AA
0.001881
AA
2157.107910
452.160431
SNP_A-1980898
AA
0.008638
AA
978.860596
357.357880
SNP_A-1983139
AA
0.000961
AA
2751.711914
722.026306
SNP_A-4265735
AA
0.001484
AA
2685.839355
778.981995
SNP_A-1995832
AA
0.004387
AA
2713.568604
719.612854
SNP_A-1995893
AA
0.003966
AA
2082.708008
1051.642700
SNP_A-1997689
BB
0.002674
BB
796.086609
3339.125732
SNP_A-1997709
AA
0.001646
AA
1567.865967
359.384796
SNP_A-1997896
AA
0.010367
AA
1466.988892
875.851624
SNP_A-1997922
AA
0.007991
AA
687.881042
321.301025
SNP_A-2000230
NC
0.574028
AA
2221.735840
1893.993530
SNP_A-2000332
AA
0.010066
AA
3265.075195
1393.577026
SNP_A-2000337
AA
0.007148
AA
1052.008423
379.521729
SNP_A-2000342
AA
0.002108
AA
3632.828857
1151.296631
SNP_A-4268173
BB
0.007267
BB
347.142090
971.349243
909622 46154 Kbytes .Supplementary file Size Download File type/resource GSM1637340_E14181_GenomeWideSNP_6_.CEL.gz
26.3 Mb
(ftp) (http) CEL
GSM1637340_E14181_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
