GEO help: Mouse over screen elements for information.
Status
Public on Feb 01, 2016
Title
blood-Control_5486
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
0.000648
AB
2924.936523
2966.613525
SNP_A-1967418
BB
0.005173
BB
402.874176
762.871948
SNP_A-1969580
BB
0.002450
BB
1245.651001
3897.977051
SNP_A-4263484
BB
0.008547
BB
538.450317
2136.554443
SNP_A-1978185
AA
0.003333
AA
1392.247925
499.956299
SNP_A-4264431
AA
0.001393
AA
2015.992188
485.048676
SNP_A-1980898
AB
0.001967
AB
777.050720
628.177124
SNP_A-1983139
AA
0.001748
AA
2991.433594
713.319397
SNP_A-4265735
AA
0.002253
AA
2247.219238
617.918335
SNP_A-1995832
AB
0.001511
AB
1545.115967
1124.925537
SNP_A-1995893
AB
0.008767
AB
1202.825439
1613.008179
SNP_A-1997689
BB
0.001465
BB
727.421570
3708.527832
SNP_A-1997709
AA
0.002899
AA
1309.185913
317.883026
SNP_A-1997896
AA
0.001534
AA
1265.789795
531.772339
SNP_A-1997922
AB
0.001932
AB
592.066467
545.088440
SNP_A-2000230
AA
0.001336
AA
2385.105469
1403.767700
SNP_A-2000332
AA
0.001820
AA
3303.327148
887.993835
SNP_A-2000337
AA
0.010259
AA
1827.763306
389.579132
SNP_A-2000342
AA
0.000853
AA
3200.475830
925.875610
SNP_A-4268173
AB
0.003702
AB
1082.959351
769.971802
909622 46153 Kbytes .Supplementary file Size Download File type/resource GSM1637405_5486_GenomeWideSNP_6_.CEL.gz
26.4 Mb
(ftp) (http) CEL
GSM1637405_5486_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
