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Status
Public on Feb 01, 2016
Title
blood-PTC_E11771
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
0.000772
AB
3433.498779
3185.014648
SNP_A-1967418
BB
0.005838
BB
270.808350
774.579224
SNP_A-1969580
BB
0.011950
BB
617.555359
2468.686523
SNP_A-4263484
BB
0.004071
BB
641.029297
2226.416992
SNP_A-1978185
AA
0.004719
AA
1938.059448
433.730072
SNP_A-4264431
AA
0.004768
AA
2201.343506
387.513245
SNP_A-1980898
BB
0.012281
BB
306.206665
1240.307007
SNP_A-1983139
AA
0.003338
AA
2666.900879
589.269226
SNP_A-4265735
AA
0.001821
AA
2796.536133
775.805603
SNP_A-1995832
AA
0.001876
AA
2510.205811
658.884460
SNP_A-1995893
AA
0.021780
AA
2189.666260
1507.057617
SNP_A-1997689
BB
0.003145
BB
705.234314
3618.562988
SNP_A-1997709
AA
0.001359
AA
1700.194458
366.798004
SNP_A-1997896
AA
0.003199
AA
1307.106079
718.145081
SNP_A-1997922
AA
0.002866
AA
851.601929
298.179718
SNP_A-2000230
AB
0.090844
AB
2481.037109
2147.110107
SNP_A-2000332
AB
0.004197
AB
2447.899414
2349.142822
SNP_A-2000337
AA
0.001117
AA
1305.206421
400.386536
SNP_A-2000342
AA
0.001701
AA
3775.380127
988.416931
SNP_A-4268173
AA
0.001371
AA
1646.693237
332.875885
909622 46142 Kbytes .Supplementary file Size Download File type/resource GSM1637336_E11771_GenomeWideSNP_6_.CEL.gz
26.4 Mb
(ftp) (http) CEL
GSM1637336_E11771_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
