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Status
Public on Feb 01, 2016
Title
blood-MTC_4487
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
0.002850
BB
795.227966
4122.489258
SNP_A-1967418
BB
0.006913
BB
260.509216
749.745239
SNP_A-1969580
BB
0.005998
BB
1377.924683
4720.809082
SNP_A-4263484
BB
0.002085
BB
543.866577
1614.655762
SNP_A-1978185
AA
0.003547
AA
1700.414307
374.354553
SNP_A-4264431
AA
0.002071
AA
1900.423096
379.397095
SNP_A-1980898
BB
0.001735
BB
367.435120
889.398193
SNP_A-1983139
AA
0.002686
AA
3277.497559
928.502991
SNP_A-4265735
AA
0.003349
AA
1946.877808
483.797455
SNP_A-1995832
AB
0.002672
AB
1402.614380
1342.456177
SNP_A-1995893
AB
0.002713
AB
1590.123413
1636.823486
SNP_A-1997689
BB
0.004382
BB
624.499939
3753.515625
SNP_A-1997709
AA
0.006706
AA
1975.301270
295.677643
SNP_A-1997896
AA
0.008629
AA
1398.803345
403.242035
SNP_A-1997922
AB
0.003973
AB
508.891205
548.174927
SNP_A-2000230
AA
0.007196
AA
2058.376709
817.933350
SNP_A-2000332
AA
0.002940
AA
3850.370850
927.775757
SNP_A-2000337
AA
0.005966
AA
1286.625122
279.834717
SNP_A-2000342
AA
0.000325
AA
3253.136475
956.469543
SNP_A-4268173
AA
0.005595
AA
1889.442383
317.200745
909622 46146 Kbytes .Supplementary file Size Download File type/resource GSM1636631_4487_GenomeWideSNP_6_.CEL.gz
27.2 Mb
(ftp) (http) CEL
GSM1636631_4487_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
