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Status
Public on Feb 01, 2016
Title
blood-Control_2149
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
0.001674
AB
3405.938965
3283.603027
SNP_A-1967418
AB
0.001705
AB
622.723572
576.386047
SNP_A-1969580
BB
0.003347
BB
935.552246
3443.719238
SNP_A-4263484
AB
0.009649
AB
1853.575928
1548.963379
SNP_A-1978185
AA
0.006538
AA
2157.740723
451.429749
SNP_A-4264431
AA
0.007733
AA
1352.036011
333.974060
SNP_A-1980898
AB
0.006513
AB
604.349243
554.246277
SNP_A-1983139
AA
0.000144
AA
2936.092285
775.757935
SNP_A-4265735
AB
0.007402
AB
996.998596
952.758240
SNP_A-1995832
AA
0.005774
AA
1824.091431
363.757660
SNP_A-1995893
AA
0.006025
AA
2708.294678
1328.758057
SNP_A-1997689
BB
0.006301
BB
835.253296
4719.733398
SNP_A-1997709
AA
0.002891
AA
2204.859619
404.880890
SNP_A-1997896
AA
0.002836
AA
1149.675415
595.076660
SNP_A-1997922
AA
0.008540
AA
892.059692
253.880615
SNP_A-2000230
AA
0.001914
AA
2240.339355
1467.023682
SNP_A-2000332
AB
0.002563
AB
2794.738037
2912.106445
SNP_A-2000337
AA
0.002141
AA
1320.906982
336.187378
SNP_A-2000342
AA
0.006166
AA
3772.247803
803.975342
SNP_A-4268173
AA
0.005659
AA
1127.001465
271.223541
909622 46134 Kbytes .Supplementary file Size Download File type/resource GSM1637449_2149_GenomeWideSNP_6_.CEL.gz
27.8 Mb
(ftp) (http) CEL
GSM1637449_2149_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
