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Status
Public on Feb 01, 2016
Title
blood-MTC_2220R
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
NC
0.190059
BB
1222.425537
2898.638428
SNP_A-1967418
BB
0.000887
BB
356.383148
778.394165
SNP_A-1969580
BB
0.009729
BB
1557.649048
4673.729492
SNP_A-4263484
AA
0.000525
AA
2387.765381
486.232605
SNP_A-1978185
AA
0.001886
AA
1765.098022
425.841278
SNP_A-4264431
AB
0.002240
AB
1406.542725
1015.363098
SNP_A-1980898
BB
0.004038
BB
406.508484
906.081543
SNP_A-1983139
AA
0.004082
AA
3275.524414
986.240234
SNP_A-4265735
AB
0.003782
AB
1506.225586
1287.793579
SNP_A-1995832
AB
0.002583
AB
1738.132324
1487.309692
SNP_A-1995893
AB
0.006187
AB
1528.927124
1470.124390
SNP_A-1997689
BB
0.012580
BB
814.752808
2082.385742
SNP_A-1997709
AA
0.006025
AA
1303.102295
389.838654
SNP_A-1997896
AB
0.003726
AB
1067.738281
1622.884644
SNP_A-1997922
AA
0.056466
AA
539.803589
316.884094
SNP_A-2000230
AA
0.001436
AA
2256.747314
1169.378662
SNP_A-2000332
BB
0.004753
BB
1643.443481
4135.064453
SNP_A-2000337
AA
0.012193
AA
935.115234
336.337189
SNP_A-2000342
AA
0.001757
AA
3102.857178
1011.637939
SNP_A-4268173
AA
0.002820
AA
1834.077271
443.909790
909622 46165 Kbytes .Supplementary file Size Download File type/resource GSM1636659_2220R_GenomeWideSNP_6_.CEL.gz
27.4 Mb
(ftp) (http) CEL
GSM1636659_2220R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.0 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
