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Sample GSM1637439 Query DataSets for GSM1637439
Status Public on Feb 01, 2016
Title blood-Control_2279
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 0.000915 AA 5012.270020 780.582153
SNP_A-1967418 AB 0.014289 AB 427.040649 429.535828
SNP_A-1969580 BB 0.002220 BB 1143.025269 3669.268311
SNP_A-4263484 BB 0.005342 BB 667.668396 2178.028076
SNP_A-1978185 AA 0.001140 AA 1493.940063 466.383728
SNP_A-4264431 AA 0.011325 AA 1325.909302 400.429260
SNP_A-1980898 BB 0.004959 BB 314.301361 786.525513
SNP_A-1983139 AB 0.000386 AB 1781.862915 1511.359619
SNP_A-4265735 AA 0.005011 AA 1444.797363 453.358337
SNP_A-1995832 AB 0.002865 AB 1618.852051 1088.614380
SNP_A-1995893 AB 0.004070 AB 1435.467773 1914.650146
SNP_A-1997689 BB 0.002127 BB 793.190613 4103.197266
SNP_A-1997709 AA 0.005201 AA 2364.606201 374.626099
SNP_A-1997896 AB 0.005226 AB 848.088745 1199.605835
SNP_A-1997922 AA 0.025234 AA 718.678406 385.031769
SNP_A-2000230 AA 0.027558 AA 1684.157593 1061.558350
SNP_A-2000332 AA 0.001751 AA 3509.384521 1073.919434
SNP_A-2000337 AA 0.007089 AA 1054.445801 356.799316
SNP_A-2000342 AA 0.002989 AA 3041.983887 837.380920
SNP_A-4268173 AB 0.007608 AB 649.563232 763.790222

Total number of rows: 909622

Table truncated, full table size 46129 Kbytes.




Supplementary file Size Download File type/resource
GSM1637439_2279_GenomeWideSNP_6_.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM1637439_2279_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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