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Status
Public on Feb 01, 2016
Title
blood-Control_4353R
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
NC
0.106689
BB
745.586182
2165.770508
SNP_A-1967418
AA
0.002390
AA
789.936035
307.259888
SNP_A-1969580
BB
0.021900
BB
1747.106323
4575.690430
SNP_A-4263484
BB
0.014811
BB
520.042847
1162.133301
SNP_A-1978185
AA
0.015630
AA
2294.521729
350.479492
SNP_A-4264431
AB
0.009512
AB
1027.254761
622.107056
SNP_A-1980898
BB
0.011709
BB
368.760803
1164.723999
SNP_A-1983139
AA
0.018161
AA
3135.427979
1192.851685
SNP_A-4265735
AA
0.008057
AA
2317.947998
956.814758
SNP_A-1995832
AB
0.008551
AB
2083.296875
1662.836060
SNP_A-1995893
AB
0.015277
AB
2076.787354
1935.839355
SNP_A-1997689
BB
0.019682
BB
582.220764
1597.782227
SNP_A-1997709
AA
0.004908
AA
1654.488037
422.518982
SNP_A-1997896
AB
0.020890
AB
1434.524292
1899.807251
SNP_A-1997922
AA
0.015038
AA
562.295471
265.850586
SNP_A-2000230
NC
0.344119
AB
1002.828308
657.211670
SNP_A-2000332
AB
0.007249
AB
2875.457764
3187.192871
SNP_A-2000337
AA
0.042693
AA
629.968140
238.323181
SNP_A-2000342
AA
0.023966
AA
2159.497803
661.812256
SNP_A-4268173
AA
0.010948
AA
2296.454346
503.460785
909622 46155 Kbytes .Supplementary file Size Download File type/resource GSM1637424_4353R_GenomeWideSNP_6_.CEL.gz
26.5 Mb
(ftp) (http) CEL
GSM1637424_4353R_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
