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Status
Public on Feb 01, 2016
Title
blood-Control_5596
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens Characteristics
phenotype: Control
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
0.000960
BB
873.545959
4801.273926
SNP_A-1967418
BB
0.002624
BB
334.068268
839.574280
SNP_A-1969580
BB
0.003957
BB
1056.441406
4343.663086
SNP_A-4263484
BB
0.003080
BB
609.024658
2030.582275
SNP_A-1978185
AA
0.001706
AA
1511.333740
483.089691
SNP_A-4264431
AA
0.005903
AA
2322.799072
489.718933
SNP_A-1980898
BB
0.000701
BB
356.514740
912.161926
SNP_A-1983139
AA
0.004344
AA
3285.492920
741.878479
SNP_A-4265735
AA
0.000045
AA
2060.860596
651.533386
SNP_A-1995832
NC
0.333663
AA
1874.758423
793.380920
SNP_A-1995893
AA
0.032724
AA
1750.522461
1039.542236
SNP_A-1997689
BB
0.003954
BB
899.680664
4403.400879
SNP_A-1997709
AA
0.005746
AA
1294.428833
263.939819
SNP_A-1997896
AA
0.004056
AA
1463.806030
701.759644
SNP_A-1997922
AA
0.008759
AA
839.574280
416.424866
SNP_A-2000230
AA
0.004319
AA
2591.794189
1527.080200
SNP_A-2000332
AA
0.003191
AA
3088.363281
933.101440
SNP_A-2000337
AA
0.009203
AA
1704.882812
472.455353
SNP_A-2000342
AA
0.011040
AA
4109.353027
1128.998291
SNP_A-4268173
AA
0.002362
AA
1356.638184
321.557037
909622 46152 Kbytes .Supplementary file Size Download File type/resource GSM1637396_5596_GenomeWideSNP_6_.CEL.gz
26.3 Mb
(ftp) (http) CEL
GSM1637396_5596_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
