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Sample GSM1636623 Query DataSets for GSM1636623
Status Public on Feb 01, 2016
Title blood-MTC_5332
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: MTC
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 0.002893 BB 674.127869 4609.543945
SNP_A-1967418 AB 0.006326 AB 506.348877 428.254578
SNP_A-1969580 BB 0.002880 BB 1202.386353 3717.703125
SNP_A-4263484 BB 0.004830 BB 676.620178 1661.598511
SNP_A-1978185 AA 0.000940 AA 1514.756836 464.103058
SNP_A-4264431 AA 0.003162 AA 1752.393188 335.799744
SNP_A-1980898 AB 0.011243 AB 877.552063 564.527954
SNP_A-1983139 AA 0.006907 AA 3627.376465 865.542419
SNP_A-4265735 AA 0.006551 AA 2158.613281 461.904297
SNP_A-1995832 AB 0.006405 AB 1174.598877 1219.684937
SNP_A-1995893 AB 0.003740 AB 1369.835327 1746.618530
SNP_A-1997689 BB 0.002525 BB 714.817444 3934.031738
SNP_A-1997709 AA 0.009258 AA 2746.146973 431.302948
SNP_A-1997896 AB 0.006984 AB 990.093384 1143.880981
SNP_A-1997922 AA 0.006165 AA 760.552185 249.406845
SNP_A-2000230 AA 0.006260 AA 2121.653809 856.823975
SNP_A-2000332 BB 0.002172 BB 1156.993408 3924.790771
SNP_A-2000337 AA 0.004735 AA 1436.060669 290.462494
SNP_A-2000342 AA 0.002585 AA 3007.866943 1008.181213
SNP_A-4268173 AA 0.002987 AA 1778.345093 326.553467

Total number of rows: 909622

Table truncated, full table size 46132 Kbytes.




Supplementary file Size Download File type/resource
GSM1636623_5332_GenomeWideSNP_6_.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM1636623_5332_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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