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Status
Public on Feb 01, 2016
Title
blood-PTC_E11024b
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
0.003706
BB
661.878662
4084.678467
SNP_A-1967418
AB
0.003713
AB
636.165222
579.650940
SNP_A-1969580
BB
0.002862
BB
1016.077881
4124.859863
SNP_A-4263484
AB
0.026787
AB
2489.350342
1570.385864
SNP_A-1978185
AA
0.003226
AA
1249.771851
372.782745
SNP_A-4264431
AB
0.008128
AB
1655.595947
1301.167725
SNP_A-1980898
BB
0.023919
BB
336.686646
1375.785278
SNP_A-1983139
AA
0.004534
AA
2516.105225
546.451355
SNP_A-4265735
AA
0.047412
AA
4417.198730
632.397705
SNP_A-1995832
AA
0.002955
AA
2012.062134
456.863617
SNP_A-1995893
AA
0.008594
AA
1885.158081
897.998169
SNP_A-1997689
BB
0.013825
BB
638.845032
2544.510986
SNP_A-1997709
AA
0.013306
AA
2126.176025
262.000122
SNP_A-1997896
AA
0.003281
AA
1489.922852
538.043274
SNP_A-1997922
AA
0.008215
AA
830.833984
240.434235
SNP_A-2000230
AA
0.059664
AA
4360.835449
1473.761108
SNP_A-2000332
AB
0.030729
AB
3637.838135
3238.102539
SNP_A-2000337
AA
0.006279
AA
1669.073730
436.092682
SNP_A-2000342
AA
0.014920
AA
4554.647461
876.497131
SNP_A-4268173
AB
0.003735
AB
1125.907227
904.401917
909622 46157 Kbytes .Supplementary file Size Download File type/resource GSM1637314_E11024b_GenomeWideSNP_6_.CEL.gz
26.4 Mb
(ftp) (http) CEL
GSM1637314_E11024b_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
