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Status
Public on Feb 01, 2016
Title
blood-Control_4271
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
0.005531
BB
890.132141
3687.747559
SNP_A-1967418
BB
0.010091
BB
296.226105
558.515564
SNP_A-1969580
BB
0.002702
BB
930.493713
3666.719238
SNP_A-4263484
AB
0.005413
AB
1786.975586
1156.810303
SNP_A-1978185
AB
0.003246
AB
1183.198975
1672.897949
SNP_A-4264431
BB
0.005167
BB
378.555542
1143.629517
SNP_A-1980898
BB
0.004091
BB
367.118561
824.577271
SNP_A-1983139
AA
0.004621
AA
2401.480957
657.969727
SNP_A-4265735
AA
0.004333
AA
1541.639038
437.624542
SNP_A-1995832
BB
0.004084
BB
691.469788
1580.634033
SNP_A-1995893
BB
0.001571
BB
495.142212
2526.137939
SNP_A-1997689
BB
0.007667
BB
744.882324
4725.119629
SNP_A-1997709
AA
0.003108
AA
1414.114014
369.433655
SNP_A-1997896
AA
0.003660
AA
1185.059814
482.621307
SNP_A-1997922
BB
0.000454
BB
472.129150
939.999268
SNP_A-2000230
AA
0.000855
AA
2198.870361
1342.482788
SNP_A-2000332
AA
0.004984
AA
3305.918457
1161.811890
SNP_A-2000337
AA
0.001358
AA
1298.224731
387.574738
SNP_A-2000342
AA
0.003239
AA
3331.027832
788.545105
SNP_A-4268173
AA
0.001125
AA
1514.552124
298.647430
909622 46138 Kbytes .Supplementary file Size Download File type/resource GSM1637425_4271_GenomeWideSNP_6_.CEL.gz
27.1 Mb
(ftp) (http) CEL
GSM1637425_4271_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
