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Status
Public on Feb 01, 2016
Title
blood-PTC_E11587
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
0.002150
BB
821.736145
4293.957031
SNP_A-1967418
NC
0.216153
AB
481.087219
717.074097
SNP_A-1969580
BB
0.007449
BB
765.960205
2699.479248
SNP_A-4263484
BB
0.009178
BB
480.052399
2113.799072
SNP_A-1978185
AA
0.011269
AA
1922.662354
627.158386
SNP_A-4264431
AA
0.024020
AA
2821.614502
391.218353
SNP_A-1980898
AB
0.006820
AB
885.499878
595.519165
SNP_A-1983139
AA
0.007588
AA
2129.880859
490.242554
SNP_A-4265735
AB
0.010977
AB
2299.312256
2388.628906
SNP_A-1995832
AB
0.012414
AB
1877.853149
1077.604736
SNP_A-1995893
AB
0.007950
AB
1252.685425
1933.479126
SNP_A-1997689
BB
0.002447
BB
854.663635
4311.269043
SNP_A-1997709
NC
0.811053
AA
1146.786865
499.393921
SNP_A-1997896
AB
0.008044
AB
1133.867432
1758.054443
SNP_A-1997922
AB
0.008359
AB
471.934998
609.181641
SNP_A-2000230
AB
0.005862
AB
2687.841064
2726.565674
SNP_A-2000332
AB
0.003721
AB
2182.820801
2528.848877
SNP_A-2000337
AA
0.002174
AA
1526.573364
393.141754
SNP_A-2000342
AA
0.001500
AA
3756.987549
994.889465
SNP_A-4268173
AB
0.004482
AB
907.553528
640.853943
909622 46151 Kbytes .Supplementary file Size Download File type/resource GSM1637334_E11587_GenomeWideSNP_6_.CEL.gz
25.1 Mb
(ftp) (http) CEL
GSM1637334_E11587_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.6 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
