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Sample GSM1636651 Query DataSets for GSM1636651
Status Public on Feb 01, 2016
Title blood-MTC_2862R
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 AB 0.017783 AB 1619.318604 2132.658203
SNP_A-1967418 BB 0.000963 BB 356.466309 758.742432
SNP_A-1969580 BB 0.019453 BB 1732.604614 5166.589355
SNP_A-4263484 AB 0.004523 AB 1372.896484 906.322571
SNP_A-1978185 AA 0.004834 AA 1890.847046 386.477600
SNP_A-4264431 AB 0.003164 AB 1163.821411 787.985962
SNP_A-1980898 BB 0.000315 BB 343.261658 912.915222
SNP_A-1983139 AA 0.012984 AA 3512.470215 1192.643066
SNP_A-4265735 AA 0.009071 AA 2296.332520 971.329590
SNP_A-1995832 BB 0.023570 BB 1020.184143 3168.362793
SNP_A-1995893 BB 0.006475 BB 688.826050 2419.904297
SNP_A-1997689 BB 0.011796 BB 596.023743 2116.002441
SNP_A-1997709 AA 0.002878 AA 1314.500122 335.757843
SNP_A-1997896 AB 0.011293 AB 1413.993408 1650.316772
SNP_A-1997922 AB 0.038692 AB 381.762177 575.838623
SNP_A-2000230 AA 0.037007 AA 1693.626587 1148.075928
SNP_A-2000332 AA 0.002832 AA 3793.625732 900.635620
SNP_A-2000337 AA 0.008766 AA 1009.550903 403.597412
SNP_A-2000342 AA 0.012166 AA 2410.619385 884.047119
SNP_A-4268173 AB 0.023997 AB 893.038940 1206.288696

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.




Supplementary file Size Download File type/resource
GSM1636651_2862R_GenomeWideSNP_6_.CEL.gz 27.0 Mb (ftp)(http) CEL
GSM1636651_2862R_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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