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Status
Public on Feb 01, 2016
Title
blood-Control_2279
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
AA
0.000915
AA
5012.270020
780.582153
SNP_A-1967418
AB
0.014289
AB
427.040649
429.535828
SNP_A-1969580
BB
0.002220
BB
1143.025269
3669.268311
SNP_A-4263484
BB
0.005342
BB
667.668396
2178.028076
SNP_A-1978185
AA
0.001140
AA
1493.940063
466.383728
SNP_A-4264431
AA
0.011325
AA
1325.909302
400.429260
SNP_A-1980898
BB
0.004959
BB
314.301361
786.525513
SNP_A-1983139
AB
0.000386
AB
1781.862915
1511.359619
SNP_A-4265735
AA
0.005011
AA
1444.797363
453.358337
SNP_A-1995832
AB
0.002865
AB
1618.852051
1088.614380
SNP_A-1995893
AB
0.004070
AB
1435.467773
1914.650146
SNP_A-1997689
BB
0.002127
BB
793.190613
4103.197266
SNP_A-1997709
AA
0.005201
AA
2364.606201
374.626099
SNP_A-1997896
AB
0.005226
AB
848.088745
1199.605835
SNP_A-1997922
AA
0.025234
AA
718.678406
385.031769
SNP_A-2000230
AA
0.027558
AA
1684.157593
1061.558350
SNP_A-2000332
AA
0.001751
AA
3509.384521
1073.919434
SNP_A-2000337
AA
0.007089
AA
1054.445801
356.799316
SNP_A-2000342
AA
0.002989
AA
3041.983887
837.380920
SNP_A-4268173
AB
0.007608
AB
649.563232
763.790222
909622 46129 Kbytes .Supplementary file Size Download File type/resource GSM1637439_2279_GenomeWideSNP_6_.CEL.gz
28.1 Mb
(ftp) (http) CEL
GSM1637439_2279_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
