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Status
Public on Feb 01, 2016
Title
blood-Control_5487
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
0.004705
BB
1060.500977
3915.291992
SNP_A-1967418
BB
0.001960
BB
327.975006
813.496582
SNP_A-1969580
BB
0.005346
BB
1416.510864
4250.148438
SNP_A-4263484
AB
0.006484
AB
1291.286011
845.786499
SNP_A-1978185
AA
0.014807
AA
841.737244
263.740936
SNP_A-4264431
AA
0.003285
AA
2139.099854
439.720428
SNP_A-1980898
NC
0.262007
AB
467.369720
689.901978
SNP_A-1983139
AA
0.002951
AA
2770.349609
628.235901
SNP_A-4265735
AB
0.001270
AB
1527.678467
1462.685791
SNP_A-1995832
AB
0.001127
AB
1571.447632
1368.669312
SNP_A-1995893
AB
0.005229
AB
1312.109741
1616.070923
SNP_A-1997689
BB
0.001272
BB
801.358459
3327.577148
SNP_A-1997709
AA
0.003787
AA
1203.492554
318.951782
SNP_A-1997896
AA
0.012137
AA
1529.764526
825.589966
SNP_A-1997922
AB
0.005094
AB
492.107239
554.731140
SNP_A-2000230
AA
0.027679
AA
1962.426758
1550.614136
SNP_A-2000332
AA
0.004619
AA
3931.784424
878.161621
SNP_A-2000337
AA
0.007627
AA
1492.046631
500.080444
SNP_A-2000342
AA
0.007511
AA
3268.512695
1232.752075
SNP_A-4268173
AA
0.008094
AA
1858.772095
264.587616
909622 46153 Kbytes .Supplementary file Size Download File type/resource GSM1637404_5487_GenomeWideSNP_6_.CEL.gz
25.2 Mb
(ftp) (http) CEL
GSM1637404_5487_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.8 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
