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Sample GSM1637453 Query DataSets for GSM1637453
Status Public on Feb 01, 2016
Title blood-Control_1790
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 0.015157 AA 7147.907227 1199.251343
SNP_A-1967418 BB 0.006302 BB 268.029114 639.799377
SNP_A-1969580 BB 0.001590 BB 1094.429810 3676.442627
SNP_A-4263484 AA 0.010314 AA 2040.887695 561.467712
SNP_A-1978185 AA 0.005392 AA 1663.656982 555.854187
SNP_A-4264431 AA 0.008144 AA 1619.548584 534.435852
SNP_A-1980898 AA 0.008633 AA 1079.774658 461.845764
SNP_A-1983139 AA 0.004740 AA 3536.696289 920.903015
SNP_A-4265735 AA 0.013951 AA 3150.343262 859.359863
SNP_A-1995832 BB 0.009619 BB 1080.870728 2691.478271
SNP_A-1995893 BB 0.002180 BB 454.221680 2354.015381
SNP_A-1997689 BB 0.005914 BB 855.440308 2731.402832
SNP_A-1997709 AA 0.002095 AA 1845.243164 404.377289
SNP_A-1997896 AB 0.008093 AB 709.369629 1176.207886
SNP_A-1997922 AB 0.010093 AB 661.566406 723.066711
SNP_A-2000230 AA 0.005190 AA 2618.401123 1592.007202
SNP_A-2000332 AB 0.002762 AB 2515.268311 2462.173828
SNP_A-2000337 AA 0.000413 AA 1376.916260 389.528168
SNP_A-2000342 AA 0.002491 AA 3528.437256 1069.615112
SNP_A-4268173 AA 0.006241 AA 1115.737671 285.458801

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM1637453_1790_GenomeWideSNP_6_.CEL.gz 29.0 Mb (ftp)(http) CEL
GSM1637453_1790_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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