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Status
Public on Feb 01, 2016
Title
blood-MTC_6278b
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
0.001135
AB
3225.339111
3282.498779
SNP_A-1967418
AB
0.012275
AB
493.319702
615.656128
SNP_A-1969580
BB
0.008810
BB
1187.402100
3298.220215
SNP_A-4263484
BB
0.004762
BB
436.221313
1549.414062
SNP_A-1978185
AA
0.003591
AA
1591.453125
362.043640
SNP_A-4264431
AB
0.002707
AB
1123.651978
1014.387695
SNP_A-1980898
AB
0.003459
AB
636.695984
622.650391
SNP_A-1983139
AA
0.005898
AA
3252.560791
1034.362915
SNP_A-4265735
AA
0.000871
AA
1908.611450
614.547852
SNP_A-1995832
AB
0.000111
AB
1540.898438
1253.359619
SNP_A-1995893
AB
0.004795
AB
1357.071045
1821.907104
SNP_A-1997689
BB
0.002293
BB
817.324585
4159.836426
SNP_A-1997709
AA
0.003875
AA
2190.533203
357.657684
SNP_A-1997896
AB
0.000945
AB
960.463074
1376.416260
SNP_A-1997922
AA
0.002473
AA
849.363770
379.213867
SNP_A-2000230
AA
0.001169
AA
2174.154785
1204.396973
SNP_A-2000332
AA
0.001369
AA
3438.294922
890.733948
SNP_A-2000337
AA
0.000377
AA
1376.232788
371.594147
SNP_A-2000342
AA
0.000318
AA
3330.425049
949.199951
SNP_A-4268173
AB
0.000789
AB
1016.598938
894.789001
909622 46139 Kbytes .Supplementary file Size Download File type/resource GSM1636614_6278b_GenomeWideSNP_6_.CEL.gz
26.9 Mb
(ftp) (http) CEL
GSM1636614_6278b_GenomeWideSNP_6_.birdseed-v2.chp.gz
12.9 Mb
(ftp) (http) CHP
Processed data included within Sample table Processed data provided as supplementary file
