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Status
Public on Feb 01, 2016
Title
blood-PTC_E11029
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
BB
0.010563
BB
634.474609
3154.700439
SNP_A-1967418
AB
0.001809
AB
591.396606
539.901062
SNP_A-1969580
BB
0.001770
BB
1119.828125
4116.323730
SNP_A-4263484
AB
0.013213
AB
1792.466431
1706.474854
SNP_A-1978185
AA
0.004177
AA
1196.447876
357.203003
SNP_A-4264431
AA
0.046342
AA
3109.762207
370.260010
SNP_A-1980898
BB
0.004196
BB
374.661530
860.769409
SNP_A-1983139
AA
0.009858
AA
1923.430298
549.217529
SNP_A-4265735
AB
0.001449
AB
1706.765503
1634.258545
SNP_A-1995832
AA
0.054265
AA
1604.440918
410.230927
SNP_A-1995893
AA
0.002737
AA
2365.980713
1268.151123
SNP_A-1997689
BB
0.010249
BB
1021.025879
4801.825684
SNP_A-1997709
AA
0.005794
AA
1588.037842
263.484985
SNP_A-1997896
AA
0.020196
AA
2006.494019
789.429016
SNP_A-1997922
AA
0.022356
AA
1276.798584
340.086700
SNP_A-2000230
AB
0.047850
AB
2609.775635
2223.571289
SNP_A-2000332
AB
0.002379
AB
2552.972656
2905.249268
SNP_A-2000337
AA
0.006487
AA
1557.693237
489.981842
SNP_A-2000342
AA
0.009100
AA
4504.053711
1094.133911
SNP_A-4268173
AA
0.004249
AA
1819.176758
396.781403
909622 46145 Kbytes .Supplementary file Size Download File type/resource GSM1637315_E11029_GenomeWideSNP_6_.CEL.gz
25.0 Mb
(ftp) (http) CEL
GSM1637315_E11029_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.7 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
