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Status
Public on Feb 01, 2016
Title
blood-Control_5935
Sample type
genomic
Source name
peripheral blood
Organism
Homo sapiens
Characteristics
phenotype: Control 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
0.025602
BB
1120.495483
7411.882324
SNP_A-1967418
BB
0.005741
BB
396.998932
899.315674
SNP_A-1969580
BB
0.005839
BB
1043.182739
3225.029053
SNP_A-4263484
BB
0.003880
BB
593.892883
1556.695435
SNP_A-1978185
AA
0.001258
AA
1435.440918
456.767853
SNP_A-4264431
BB
0.006377
BB
590.222961
1707.928101
SNP_A-1980898
AB
0.003943
AB
818.812195
620.353027
SNP_A-1983139
AA
0.001374
AA
3177.148193
854.249817
SNP_A-4265735
AA
0.016031
AA
3264.176758
922.163391
SNP_A-1995832
AB
0.008557
AB
2092.811523
1635.524902
SNP_A-1995893
AB
0.009340
AB
1936.414795
2159.980225
SNP_A-1997689
BB
0.004698
BB
923.915833
3117.164307
SNP_A-1997709
AA
0.003314
AA
2001.870605
427.149658
SNP_A-1997896
AA
0.002515
AA
1263.250488
656.322571
SNP_A-1997922
AB
0.006851
AB
647.995911
699.203735
SNP_A-2000230
AA
0.002086
AA
2397.983398
1492.599243
SNP_A-2000332
BB
0.001656
BB
1251.979736
3698.267578
SNP_A-2000337
AA
0.001100
AA
1388.313965
408.488953
SNP_A-2000342
AA
0.000248
AA
3277.034668
976.028320
SNP_A-4268173
AA
0.005485
AA
1146.111450
284.326416
Total number of rows: 909622 Table truncated, full table size 46133 Kbytes .Supplementary file
Size
Download
File type/resource
GSM1637376_5935_GenomeWideSNP_6_.CEL.gz
28.9 Mb
(ftp) (http)
CEL
GSM1637376_5935_GenomeWideSNP_6_.birdseed-v2.chp.gz
13.1 Mb
(ftp) (http)
CHP
Processed data included within Sample table
Processed data provided as supplementary file