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Status
Public on Feb 01, 2016
Title
blood-Control_2209
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
0.005745
BB
860.438293
5776.666992
SNP_A-1967418
BB
0.002532
BB
348.274109
690.024292
SNP_A-1969580
BB
0.012371
BB
632.860779
3563.487793
SNP_A-4263484
AB
0.005272
AB
1564.216797
1389.952148
SNP_A-1978185
AA
0.008709
AA
1600.135620
297.442291
SNP_A-4264431
NC
0.293185
AA
1295.063965
528.083923
SNP_A-1980898
AB
0.009824
AB
924.268982
674.712036
SNP_A-1983139
AA
0.016646
AA
3799.564697
749.738098
SNP_A-4265735
AB
0.000312
AB
1371.421021
1427.029297
SNP_A-1995832
AB
0.005211
AB
1398.183228
889.178772
SNP_A-1995893
AB
0.003498
AB
1718.816162
1722.383179
SNP_A-1997689
BB
0.003012
BB
803.191711
4265.804688
SNP_A-1997709
AA
0.007040
AA
2066.040283
303.273407
SNP_A-1997896
AA
0.011977
AA
1057.372314
358.885956
SNP_A-1997922
AA
0.026399
AA
616.758240
332.813141
SNP_A-2000230
AA
0.002815
AA
2050.554688
1131.486694
SNP_A-2000332
AB
0.002966
AB
2268.313477
2609.921387
SNP_A-2000337
AA
0.001299
AA
1476.472534
362.141846
SNP_A-2000342
AA
0.010589
AA
3825.396973
679.842651
SNP_A-4268173
AB
0.002706
AB
817.496033
807.972717
909622 46135 Kbytes .Supplementary file Size Download File type/resource GSM1637444_2209_GenomeWideSNP_6_.CEL.gz
24.9 Mb
(ftp) (http) CEL
GSM1637444_2209_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.7 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
