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Status
Public on Feb 01, 2016
Title
blood-MTC_4267R
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens Characteristics
phenotype: MTC
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
0.010984
AA
4335.460449
1442.714966
SNP_A-1967418
BB
0.010526
BB
427.923187
951.545288
SNP_A-1969580
BB
0.007138
BB
992.448853
3093.990723
SNP_A-4263484
BB
0.014394
BB
888.774597
2363.353027
SNP_A-1978185
AA
0.024286
AA
2584.858154
652.268066
SNP_A-4264431
AB
0.000586
AB
1241.621582
920.826294
SNP_A-1980898
AB
0.006613
AB
723.641602
516.678284
SNP_A-1983139
AA
0.058623
AA
3118.450439
1443.441650
SNP_A-4265735
AA
0.004413
AA
2022.967896
804.699158
SNP_A-1995832
BB
0.001612
BB
825.691467
1909.596802
SNP_A-1995893
BB
0.022735
BB
833.823853
3219.772705
SNP_A-1997689
BB
0.019593
BB
1262.449829
4386.042480
SNP_A-1997709
AA
0.007189
AA
1492.450806
425.779022
SNP_A-1997896
AB
0.004323
AB
1139.131836
1636.062744
SNP_A-1997922
AB
0.006089
AB
673.506348
702.613525
SNP_A-2000230
AA
0.032820
AA
2206.325195
1899.670410
SNP_A-2000332
BB
0.029301
BB
1656.245483
3298.933350
SNP_A-2000337
AA
0.006035
AA
1174.763916
453.619476
SNP_A-2000342
NC
0.160193
AA
2947.890137
1403.266968
SNP_A-4268173
AA
0.008325
AA
1460.741089
478.282440
909622 46137 Kbytes .Supplementary file Size Download File type/resource GSM1636633_4267R_GenomeWideSNP_6_.CEL.gz
29.0 Mb
(ftp) (http) CEL
GSM1636633_4267R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
