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Status
Public on Feb 01, 2016
Title
blood-PTC_E11039
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
0.002450
AB
3144.463623
2732.493164
SNP_A-1967418
AB
0.005102
AB
614.432617
677.727661
SNP_A-1969580
BB
0.008150
BB
928.582397
2735.008301
SNP_A-4263484
BB
0.010476
BB
733.771606
2532.462891
SNP_A-1978185
AA
0.019848
AA
2609.687500
582.776855
SNP_A-4264431
AB
0.006505
AB
1407.587402
1281.857178
SNP_A-1980898
BB
0.013254
BB
299.805054
1248.343140
SNP_A-1983139
AA
0.001851
AA
3013.208740
835.642944
SNP_A-4265735
AA
0.006521
AA
3401.607422
839.490723
SNP_A-1995832
BB
0.036873
BB
1157.589844
1790.696899
SNP_A-1995893
BB
0.011326
BB
659.413940
3200.307129
SNP_A-1997689
BB
0.004171
BB
701.721008
4176.305176
SNP_A-1997709
AA
0.002112
AA
1494.269287
299.805054
SNP_A-1997896
AA
0.011085
AA
1793.180054
795.350037
SNP_A-1997922
BB
0.003749
BB
598.618103
1073.802734
SNP_A-2000230
NC
0.431582
AB
2546.769287
2040.860352
SNP_A-2000332
BB
0.025689
BB
2127.511963
4962.070801
SNP_A-2000337
AA
0.001718
AA
1403.671387
435.856415
SNP_A-2000342
AA
0.024156
AA
4492.521484
1595.467407
SNP_A-4268173
AA
0.010469
AA
1941.461060
478.945923
909622 46148 Kbytes .Supplementary file Size Download File type/resource GSM1637316_E11039_GenomeWideSNP_6_.CEL.gz
26.4 Mb
(ftp) (http) CEL
GSM1637316_E11039_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
