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Status
Public on Feb 01, 2016
Title
blood-Control_6446
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
0.002221
BB
959.303040
5325.419434
SNP_A-1967418
BB
0.002663
BB
329.401794
671.555237
SNP_A-1969580
BB
0.020010
BB
864.110657
2526.512451
SNP_A-4263484
BB
0.007938
BB
706.598389
2291.197998
SNP_A-1978185
AA
0.002321
AA
1774.336670
497.100433
SNP_A-4264431
AA
0.004318
AA
1520.698242
398.229858
SNP_A-1980898
BB
0.009345
BB
266.699158
738.841431
SNP_A-1983139
AA
0.004199
AA
2622.093262
576.390320
SNP_A-4265735
AA
0.002498
AA
1871.689575
500.523712
SNP_A-1995832
AB
0.001364
AB
1497.479736
1119.757690
SNP_A-1995893
AB
0.002770
AB
1749.466064
1928.333618
SNP_A-1997689
BB
0.006249
BB
822.823486
4704.036133
SNP_A-1997709
AA
0.002809
AA
2137.336426
367.272888
SNP_A-1997896
AA
0.001696
AA
1337.953247
648.372314
SNP_A-1997922
AB
0.013948
AB
853.738342
623.702881
SNP_A-2000230
AB
0.007378
AB
1565.645752
2805.477783
SNP_A-2000332
AB
0.003693
AB
2422.915771
2407.871094
SNP_A-2000337
AA
0.004136
AA
1240.286255
315.354919
SNP_A-2000342
AA
0.002114
AA
3567.793701
938.382446
SNP_A-4268173
AB
0.005737
AB
677.443909
715.408081
909622 46136 Kbytes .Supplementary file Size Download File type/resource GSM1637355_6446_GenomeWideSNP_6_.CEL.gz
27.8 Mb
(ftp) (http) CEL
GSM1637355_6446_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
