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Sample GSM1637403 Query DataSets for GSM1637403
Status Public on Feb 01, 2016
Title blood-Control_5489
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 AB 0.000852 AB 2873.293701 2996.748291
SNP_A-1967418 BB 0.006953 BB 418.431213 778.998596
SNP_A-1969580 BB 0.006946 BB 1110.998535 4663.694824
SNP_A-4263484 AB 0.003710 AB 1325.507446 1096.804565
SNP_A-1978185 AA 0.005780 AA 1059.010010 361.043182
SNP_A-4264431 AA 0.001489 AA 2025.611084 486.805145
SNP_A-1980898 AB 0.001856 AB 674.547974 654.805786
SNP_A-1983139 AA 0.002252 AA 2773.322021 654.895325
SNP_A-4265735 AB 0.002045 AB 1614.073730 1519.306519
SNP_A-1995832 AB 0.095121 AB 1524.241699 702.185730
SNP_A-1995893 AA 0.011806 AA 1915.661621 782.427124
SNP_A-1997689 BB 0.003315 BB 727.641113 4138.919434
SNP_A-1997709 AA 0.005603 AA 1202.285034 267.922302
SNP_A-1997896 AA 0.000799 AA 1373.719482 613.522522
SNP_A-1997922 AA 0.003043 AA 826.660034 381.351746
SNP_A-2000230 AA 0.002165 AA 2466.290527 1399.063721
SNP_A-2000332 AA 0.000995 AA 3355.374268 942.120483
SNP_A-2000337 AA 0.006415 AA 1697.403564 340.345581
SNP_A-2000342 AA 0.009316 AA 3747.269775 1260.827515
SNP_A-4268173 AB 0.002480 AB 819.793945 709.851929

Total number of rows: 909622

Table truncated, full table size 46153 Kbytes.




Supplementary file Size Download File type/resource
GSM1637403_5489_GenomeWideSNP_6_.CEL.gz 26.5 Mb (ftp)(http) CEL
GSM1637403_5489_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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