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Status
Public on Feb 01, 2016
Title
blood-Control_1648
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
0.004383
AA
4289.567383
931.183289
SNP_A-1967418
BB
0.061004
BB
275.540833
412.137482
SNP_A-1969580
BB
0.029690
BB
963.607788
2568.596191
SNP_A-4263484
AB
0.053172
AB
2221.940674
2056.700684
SNP_A-1978185
AA
0.003869
AA
1244.755859
477.834808
SNP_A-4264431
NC
0.104806
AA
915.925476
307.826935
SNP_A-1980898
BB
0.015501
BB
313.504547
656.577881
SNP_A-1983139
AA
0.084360
AA
5292.583496
1661.077515
SNP_A-4265735
AA
0.026835
AA
2857.347656
477.376617
SNP_A-1995832
BB
0.002835
BB
579.408264
1944.495361
SNP_A-1995893
BB
0.004930
BB
687.507324
2670.199951
SNP_A-1997689
BB
0.005171
BB
1014.352539
3787.854248
SNP_A-1997709
AA
0.003178
AA
1729.714233
307.826935
SNP_A-1997896
AA
0.052048
AA
693.536316
687.507324
SNP_A-1997922
AB
0.010768
AB
492.295959
472.046112
SNP_A-2000230
AA
0.012308
AA
1932.620239
1380.175293
SNP_A-2000332
BB
0.003386
BB
1594.217529
3998.332520
SNP_A-2000337
AA
0.008727
AA
1557.036743
258.783539
SNP_A-2000342
AA
0.004207
AA
2843.137207
968.334473
SNP_A-4268173
NC
0.232319
AB
418.706421
235.933151
909622 46109 Kbytes .Supplementary file Size Download File type/resource GSM1637454_1648_GenomeWideSNP_6_.CEL.gz
25.2 Mb
(ftp) (http) CEL
GSM1637454_1648_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
