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Sample GSM1637454 Query DataSets for GSM1637454
Status Public on Feb 01, 2016
Title blood-Control_1648
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 Y├║fera, 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 AA 0.004383 AA 4289.567383 931.183289
SNP_A-1967418 BB 0.061004 BB 275.540833 412.137482
SNP_A-1969580 BB 0.029690 BB 963.607788 2568.596191
SNP_A-4263484 AB 0.053172 AB 2221.940674 2056.700684
SNP_A-1978185 AA 0.003869 AA 1244.755859 477.834808
SNP_A-4264431 NC 0.104806 AA 915.925476 307.826935
SNP_A-1980898 BB 0.015501 BB 313.504547 656.577881
SNP_A-1983139 AA 0.084360 AA 5292.583496 1661.077515
SNP_A-4265735 AA 0.026835 AA 2857.347656 477.376617
SNP_A-1995832 BB 0.002835 BB 579.408264 1944.495361
SNP_A-1995893 BB 0.004930 BB 687.507324 2670.199951
SNP_A-1997689 BB 0.005171 BB 1014.352539 3787.854248
SNP_A-1997709 AA 0.003178 AA 1729.714233 307.826935
SNP_A-1997896 AA 0.052048 AA 693.536316 687.507324
SNP_A-1997922 AB 0.010768 AB 492.295959 472.046112
SNP_A-2000230 AA 0.012308 AA 1932.620239 1380.175293
SNP_A-2000332 BB 0.003386 BB 1594.217529 3998.332520
SNP_A-2000337 AA 0.008727 AA 1557.036743 258.783539
SNP_A-2000342 AA 0.004207 AA 2843.137207 968.334473
SNP_A-4268173 NC 0.232319 AB 418.706421 235.933151

Total number of rows: 909622

Table truncated, full table size 46109 Kbytes.




Supplementary file Size Download File type/resource
GSM1637454_1648_GenomeWideSNP_6_.CEL.gz 25.2 Mb (ftp)(http) CEL
GSM1637454_1648_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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