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Status
Public on Feb 01, 2016
Title
blood-Control_5489
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
AB
0.000852
AB
2873.293701
2996.748291
SNP_A-1967418
BB
0.006953
BB
418.431213
778.998596
SNP_A-1969580
BB
0.006946
BB
1110.998535
4663.694824
SNP_A-4263484
AB
0.003710
AB
1325.507446
1096.804565
SNP_A-1978185
AA
0.005780
AA
1059.010010
361.043182
SNP_A-4264431
AA
0.001489
AA
2025.611084
486.805145
SNP_A-1980898
AB
0.001856
AB
674.547974
654.805786
SNP_A-1983139
AA
0.002252
AA
2773.322021
654.895325
SNP_A-4265735
AB
0.002045
AB
1614.073730
1519.306519
SNP_A-1995832
AB
0.095121
AB
1524.241699
702.185730
SNP_A-1995893
AA
0.011806
AA
1915.661621
782.427124
SNP_A-1997689
BB
0.003315
BB
727.641113
4138.919434
SNP_A-1997709
AA
0.005603
AA
1202.285034
267.922302
SNP_A-1997896
AA
0.000799
AA
1373.719482
613.522522
SNP_A-1997922
AA
0.003043
AA
826.660034
381.351746
SNP_A-2000230
AA
0.002165
AA
2466.290527
1399.063721
SNP_A-2000332
AA
0.000995
AA
3355.374268
942.120483
SNP_A-2000337
AA
0.006415
AA
1697.403564
340.345581
SNP_A-2000342
AA
0.009316
AA
3747.269775
1260.827515
SNP_A-4268173
AB
0.002480
AB
819.793945
709.851929
909622 46153 Kbytes .Supplementary file Size Download File type/resource GSM1637403_5489_GenomeWideSNP_6_.CEL.gz
26.5 Mb
(ftp) (http) CEL
GSM1637403_5489_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
