NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1637469 Query DataSets for GSM1637469
Status Public on Feb 01, 2016
Title blood-Control_6252
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 BB 0.002110 BB 1185.845093 5285.969727
SNP_A-1967418 BB 0.001614 BB 346.413879 710.838135
SNP_A-1969580 BB 0.001301 BB 1112.174316 4145.509766
SNP_A-4263484 AB 0.003014 AB 1634.179321 1071.717773
SNP_A-1978185 AA 0.005601 AA 1020.363342 396.190430
SNP_A-4264431 AA 0.004145 AA 2142.615234 412.949707
SNP_A-1980898 AB 0.003738 AB 788.517700 755.233826
SNP_A-1983139 AA 0.003561 AA 3059.353271 675.262146
SNP_A-4265735 BB 0.003738 BB 585.507385 2049.825928
SNP_A-1995832 AA 0.070704 AA 1817.825562 656.389587
SNP_A-1995893 AA 0.004817 AA 2125.046631 932.447571
SNP_A-1997689 BB 0.001739 BB 862.460815 4023.133057
SNP_A-1997709 AA 0.007239 AA 1546.745728 257.130951
SNP_A-1997896 AA 0.000584 AA 1306.294800 562.586182
SNP_A-1997922 AA 0.009251 AA 909.968628 441.765625
SNP_A-2000230 AA 0.007371 AA 2692.742920 1688.715820
SNP_A-2000332 BB 0.000741 BB 1401.967651 3928.500732
SNP_A-2000337 AA 0.006537 AA 1721.521973 364.970490
SNP_A-2000342 AA 0.005803 AA 3870.646973 1042.405762
SNP_A-4268173 AA 0.004394 AA 1463.361206 214.553497

Total number of rows: 909622

Table truncated, full table size 46156 Kbytes.




Supplementary file Size Download File type/resource
GSM1637469_6252_GenomeWideSNP_6_.CEL.gz 25.4 Mb (ftp)(http) CEL
GSM1637469_6252_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap