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Status
Public on Feb 01, 2016
Title
blood-MTC_5332
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
BB
0.002893
BB
674.127869
4609.543945
SNP_A-1967418
AB
0.006326
AB
506.348877
428.254578
SNP_A-1969580
BB
0.002880
BB
1202.386353
3717.703125
SNP_A-4263484
BB
0.004830
BB
676.620178
1661.598511
SNP_A-1978185
AA
0.000940
AA
1514.756836
464.103058
SNP_A-4264431
AA
0.003162
AA
1752.393188
335.799744
SNP_A-1980898
AB
0.011243
AB
877.552063
564.527954
SNP_A-1983139
AA
0.006907
AA
3627.376465
865.542419
SNP_A-4265735
AA
0.006551
AA
2158.613281
461.904297
SNP_A-1995832
AB
0.006405
AB
1174.598877
1219.684937
SNP_A-1995893
AB
0.003740
AB
1369.835327
1746.618530
SNP_A-1997689
BB
0.002525
BB
714.817444
3934.031738
SNP_A-1997709
AA
0.009258
AA
2746.146973
431.302948
SNP_A-1997896
AB
0.006984
AB
990.093384
1143.880981
SNP_A-1997922
AA
0.006165
AA
760.552185
249.406845
SNP_A-2000230
AA
0.006260
AA
2121.653809
856.823975
SNP_A-2000332
BB
0.002172
BB
1156.993408
3924.790771
SNP_A-2000337
AA
0.004735
AA
1436.060669
290.462494
SNP_A-2000342
AA
0.002585
AA
3007.866943
1008.181213
SNP_A-4268173
AA
0.002987
AA
1778.345093
326.553467
909622 46132 Kbytes .Supplementary file Size Download File type/resource GSM1636623_5332_GenomeWideSNP_6_.CEL.gz
26.4 Mb
(ftp) (http) CEL
GSM1636623_5332_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
