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Status
Public on Feb 01, 2016
Title
blood-MTC_10538
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
0.014990
BB
927.984436
3169.592041
SNP_A-1967418
AB
0.030645
AB
775.130310
595.402344
SNP_A-1969580
BB
0.011374
BB
1542.060425
5013.658203
SNP_A-4263484
AB
0.001498
AB
1611.859985
1125.257568
SNP_A-1978185
AA
0.005412
AA
1818.954346
362.259186
SNP_A-4264431
AA
0.017134
AA
2700.270020
537.796448
SNP_A-1980898
AB
0.021870
AB
980.336975
871.498779
SNP_A-1983139
AA
0.000349
AA
3023.742676
795.656006
SNP_A-4265735
AA
0.002029
AA
2373.763184
738.345764
SNP_A-1995832
AB
0.011864
AB
2127.823486
1839.767822
SNP_A-1995893
AB
0.004708
AB
1816.696533
2024.602539
SNP_A-1997689
BB
0.007836
BB
634.056641
2443.565674
SNP_A-1997709
AA
0.004006
AA
1251.024414
292.030426
SNP_A-1997896
AB
0.040361
AB
1604.916504
2047.185913
SNP_A-1997922
AA
0.009484
AA
622.667114
288.342072
SNP_A-2000230
AA
0.004962
AA
2519.392822
1119.855103
SNP_A-2000332
AB
0.018927
AB
3386.192871
3361.513184
SNP_A-2000337
AA
0.007532
AA
1209.793701
483.185638
SNP_A-2000342
AA
0.007038
AA
2779.540283
1080.154419
SNP_A-4268173
AA
0.020312
AA
2564.437988
566.338867
909622 46164 Kbytes .Supplementary file Size Download File type/resource GSM1636599_10538_GenomeWideSNP_6_.CEL.gz
26.7 Mb
(ftp) (http) CEL
GSM1636599_10538_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
