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Status
Public on Feb 01, 2016
Title
blood-MTC_2118R
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens
Characteristics
phenotype: MTC tissue: peripheral blood
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
0.010280
BB
856.711975
3286.881104
SNP_A-1967418
BB
0.004701
BB
385.030182
888.526306
SNP_A-1969580
BB
0.009932
BB
1542.292236
4837.079590
SNP_A-4263484
BB
0.002467
BB
504.703674
1766.067627
SNP_A-1978185
AA
0.000844
AA
1649.645020
429.351990
SNP_A-4264431
AB
0.004778
AB
1533.127197
1065.572388
SNP_A-1980898
BB
0.007426
BB
345.392548
1103.376221
SNP_A-1983139
AA
0.006967
AA
3440.754395
1074.009033
SNP_A-4265735
BB
0.002805
BB
873.325745
2012.607788
SNP_A-1995832
BB
0.011762
BB
835.037231
2762.602051
SNP_A-1995893
BB
0.001616
BB
541.441956
2610.043213
SNP_A-1997689
BB
0.003679
BB
751.011597
2875.718750
SNP_A-1997709
AA
0.004970
AA
1087.467896
306.346069
SNP_A-1997896
AB
0.015244
AB
1484.243530
1394.683228
SNP_A-1997922
AB
0.001191
AB
576.309875
570.703674
SNP_A-2000230
AA
0.000745
AA
2246.071533
1231.082275
SNP_A-2000332
AB
0.001097
AB
2443.546143
2685.708984
SNP_A-2000337
AA
0.012574
AA
913.018188
382.793488
SNP_A-2000342
AA
0.003740
AA
3689.199951
1061.035889
SNP_A-4268173
AA
0.005228
AA
2037.785278
454.001984
Total number of rows: 909622 Table truncated, full table size 46156 Kbytes .Supplementary file
Size
Download
File type/resource
GSM1636661_2118R_GenomeWideSNP_6_.CEL.gz
28.0 Mb
(ftp) (http)
CEL
GSM1636661_2118R_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http)
CHP
Processed data included within Sample table
Processed data provided as supplementary file