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Status
Public on Feb 01, 2016
Title
blood-MTC_9512
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
0.001431
BB
1174.900635
4921.821289
SNP_A-1967418
BB
0.005515
BB
268.447937
683.638733
SNP_A-1969580
BB
0.001813
BB
988.630371
3678.436768
SNP_A-4263484
BB
0.003051
BB
589.958801
1591.909912
SNP_A-1978185
AA
0.002078
AA
1319.676270
445.193481
SNP_A-4264431
AA
0.004750
AA
2200.017578
427.738800
SNP_A-1980898
BB
0.006736
BB
356.722137
768.633362
SNP_A-1983139
AA
0.011159
AA
1989.505493
558.984009
SNP_A-4265735
AB
0.006497
AB
1036.497559
990.015991
SNP_A-1995832
AA
0.002349
AA
2470.633789
516.597534
SNP_A-1995893
AA
0.003176
AA
2658.784912
1057.012329
SNP_A-1997689
BB
0.006262
BB
619.283081
2688.234375
SNP_A-1997709
AA
0.003010
AA
1950.316650
421.673340
SNP_A-1997896
AA
0.001047
AA
1256.649780
556.893311
SNP_A-1997922
AA
0.006961
AA
673.970093
318.397064
SNP_A-2000230
AA
0.007932
AA
2041.746826
788.071167
SNP_A-2000332
AB
0.013970
AB
3317.515869
3225.072754
SNP_A-2000337
AA
0.001919
AA
1529.701782
387.034363
SNP_A-2000342
AA
0.003633
AA
2903.236328
886.628418
SNP_A-4268173
AA
0.001553
AA
1444.401123
284.311554
909622 46143 Kbytes .Supplementary file Size Download File type/resource GSM1636602_9512_GenomeWideSNP_6_.CEL.gz
27.1 Mb
(ftp) (http) CEL
GSM1636602_9512_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
