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Sample GSM1637425 Query DataSets for GSM1637425
Status Public on Feb 01, 2016
Title blood-Control_4271
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 0.005531 BB 890.132141 3687.747559
SNP_A-1967418 BB 0.010091 BB 296.226105 558.515564
SNP_A-1969580 BB 0.002702 BB 930.493713 3666.719238
SNP_A-4263484 AB 0.005413 AB 1786.975586 1156.810303
SNP_A-1978185 AB 0.003246 AB 1183.198975 1672.897949
SNP_A-4264431 BB 0.005167 BB 378.555542 1143.629517
SNP_A-1980898 BB 0.004091 BB 367.118561 824.577271
SNP_A-1983139 AA 0.004621 AA 2401.480957 657.969727
SNP_A-4265735 AA 0.004333 AA 1541.639038 437.624542
SNP_A-1995832 BB 0.004084 BB 691.469788 1580.634033
SNP_A-1995893 BB 0.001571 BB 495.142212 2526.137939
SNP_A-1997689 BB 0.007667 BB 744.882324 4725.119629
SNP_A-1997709 AA 0.003108 AA 1414.114014 369.433655
SNP_A-1997896 AA 0.003660 AA 1185.059814 482.621307
SNP_A-1997922 BB 0.000454 BB 472.129150 939.999268
SNP_A-2000230 AA 0.000855 AA 2198.870361 1342.482788
SNP_A-2000332 AA 0.004984 AA 3305.918457 1161.811890
SNP_A-2000337 AA 0.001358 AA 1298.224731 387.574738
SNP_A-2000342 AA 0.003239 AA 3331.027832 788.545105
SNP_A-4268173 AA 0.001125 AA 1514.552124 298.647430

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.




Supplementary file Size Download File type/resource
GSM1637425_4271_GenomeWideSNP_6_.CEL.gz 27.1 Mb (ftp)(http) CEL
GSM1637425_4271_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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