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Status
Public on Feb 01, 2016
Title
blood-MTC_4223R
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
0.001462
AB
2850.350830
2782.143066
SNP_A-1967418
BB
0.004114
BB
398.623932
807.052734
SNP_A-1969580
BB
0.009126
BB
1096.515991
3126.125488
SNP_A-4263484
BB
0.009541
BB
812.384277
2296.241699
SNP_A-1978185
AA
0.017236
AA
2205.925537
653.453979
SNP_A-4264431
AB
0.001400
AB
1193.057495
867.340698
SNP_A-1980898
BB
0.000341
BB
341.169006
936.492188
SNP_A-1983139
AA
0.013305
AA
3199.273682
1151.328979
SNP_A-4265735
AA
0.008945
AA
2292.633301
968.330139
SNP_A-1995832
AA
0.004171
AA
2710.196777
676.060120
SNP_A-1995893
AA
0.006537
AA
2509.995361
1335.817505
SNP_A-1997689
BB
0.003274
BB
916.633667
4234.540527
SNP_A-1997709
AA
0.030512
AA
2668.192139
598.781067
SNP_A-1997896
AA
0.004203
AA
1413.005127
711.790222
SNP_A-1997922
AA
0.002214
AA
879.994446
336.309662
SNP_A-2000230
AA
0.009790
AA
2144.298096
1651.425049
SNP_A-2000332
AB
0.005832
AB
2455.960449
2285.628418
SNP_A-2000337
AA
0.007824
AA
1118.059814
459.946442
SNP_A-2000342
AA
0.010433
AA
3341.657471
1281.699707
SNP_A-4268173
AB
0.000728
AB
1022.062012
846.386353
909622 46138 Kbytes .Supplementary file Size Download File type/resource GSM1636634_4223R_GenomeWideSNP_6_.CEL.gz
29.2 Mb
(ftp) (http) CEL
GSM1636634_4223R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
