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Status
Public on Feb 01, 2016
Title
blood-PTC_E11205
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
AB
0.006114
AB
2762.735840
2315.912109
SNP_A-1967418
BB
0.007203
BB
273.321869
824.104248
SNP_A-1969580
BB
0.003039
BB
843.271484
3381.932129
SNP_A-4263484
AB
0.002301
AB
1845.297485
1348.618774
SNP_A-1978185
AA
0.009287
AA
2205.519043
564.118286
SNP_A-4264431
AB
0.002971
AB
1430.562988
1157.314819
SNP_A-1980898
AB
0.003448
AB
713.143433
564.118286
SNP_A-1983139
AA
0.004892
AA
2667.802734
829.610535
SNP_A-4265735
AA
0.003504
AA
3009.591553
736.054138
SNP_A-1995832
NC
0.314735
AB
1061.544556
1326.704590
SNP_A-1995893
BB
0.003185
BB
496.225372
2792.307861
SNP_A-1997689
BB
0.000559
BB
840.526855
3752.685791
SNP_A-1997709
AA
0.001741
AA
1406.073364
312.147186
SNP_A-1997896
BB
0.006363
BB
662.149597
2715.421143
SNP_A-1997922
AA
0.010410
AA
772.614380
373.249512
SNP_A-2000230
NC
0.751157
AB
2607.642334
2010.163574
SNP_A-2000332
AB
0.004127
AB
2866.418213
2912.210449
SNP_A-2000337
AA
0.010869
AA
1025.019531
475.769135
SNP_A-2000342
AA
0.008503
AA
4154.917969
1348.618774
SNP_A-4268173
AB
0.002036
AB
909.060730
851.480774
909622 46157 Kbytes .Supplementary file Size Download File type/resource GSM1637326_E11205_GenomeWideSNP_6_.CEL.gz
26.3 Mb
(ftp) (http) CEL
GSM1637326_E11205_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
