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Status
Public on Feb 01, 2016
Title
blood-MTC_2862R
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
0.017783
AB
1619.318604
2132.658203
SNP_A-1967418
BB
0.000963
BB
356.466309
758.742432
SNP_A-1969580
BB
0.019453
BB
1732.604614
5166.589355
SNP_A-4263484
AB
0.004523
AB
1372.896484
906.322571
SNP_A-1978185
AA
0.004834
AA
1890.847046
386.477600
SNP_A-4264431
AB
0.003164
AB
1163.821411
787.985962
SNP_A-1980898
BB
0.000315
BB
343.261658
912.915222
SNP_A-1983139
AA
0.012984
AA
3512.470215
1192.643066
SNP_A-4265735
AA
0.009071
AA
2296.332520
971.329590
SNP_A-1995832
BB
0.023570
BB
1020.184143
3168.362793
SNP_A-1995893
BB
0.006475
BB
688.826050
2419.904297
SNP_A-1997689
BB
0.011796
BB
596.023743
2116.002441
SNP_A-1997709
AA
0.002878
AA
1314.500122
335.757843
SNP_A-1997896
AB
0.011293
AB
1413.993408
1650.316772
SNP_A-1997922
AB
0.038692
AB
381.762177
575.838623
SNP_A-2000230
AA
0.037007
AA
1693.626587
1148.075928
SNP_A-2000332
AA
0.002832
AA
3793.625732
900.635620
SNP_A-2000337
AA
0.008766
AA
1009.550903
403.597412
SNP_A-2000342
AA
0.012166
AA
2410.619385
884.047119
SNP_A-4268173
AB
0.023997
AB
893.038940
1206.288696
909622 46144 Kbytes .Supplementary file Size Download File type/resource GSM1636651_2862R_GenomeWideSNP_6_.CEL.gz
27.0 Mb
(ftp) (http) CEL
GSM1636651_2862R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
