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Status
Public on Feb 01, 2016
Title
blood-MTC_2237R
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
AB
0.014922
AB
2291.065918
1632.092163
SNP_A-1967418
BB
0.009912
BB
284.575745
556.824646
SNP_A-1969580
BB
0.004488
BB
1386.121948
4404.654785
SNP_A-4263484
BB
0.038319
BB
719.464172
1181.828247
SNP_A-1978185
AA
0.008100
AA
1675.292114
310.141968
SNP_A-4264431
AA
0.005793
AA
2090.320068
601.379700
SNP_A-1980898
BB
0.004463
BB
417.877411
957.464111
SNP_A-1983139
AA
0.005976
AA
2790.980469
927.616638
SNP_A-4265735
AA
0.007879
AA
1742.158325
774.747742
SNP_A-1995832
BB
0.000624
BB
798.112305
2027.816895
SNP_A-1995893
BB
0.009258
BB
621.813782
2117.670654
SNP_A-1997689
BB
0.008981
BB
619.241028
2343.711914
SNP_A-1997709
AA
0.007054
AA
951.368164
271.816437
SNP_A-1997896
AA
0.017878
AA
1885.367554
749.059021
SNP_A-1997922
AB
0.006873
AB
464.275299
539.965210
SNP_A-2000230
AA
0.084735
AA
1707.690308
1312.478760
SNP_A-2000332
AB
0.013699
AB
3132.039551
3348.958496
SNP_A-2000337
NC
0.717831
AB
1037.946655
631.051819
SNP_A-2000342
AA
0.007774
AA
2637.809082
994.529114
SNP_A-4268173
AA
0.014845
AA
2289.901855
384.374237
909622 46171 Kbytes .Supplementary file Size Download File type/resource GSM1636658_2237R_GenomeWideSNP_6_.CEL.gz
26.1 Mb
(ftp) (http) CEL
GSM1636658_2237R_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
