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Sample GSM1636622 Query DataSets for GSM1636622
Status Public on Feb 01, 2016
Title blood-MTC_5345R
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 0.002958 BB 1169.423218 4349.523926
SNP_A-1967418 AA 0.000695 AA 811.291565 345.718781
SNP_A-1969580 BB 0.009018 BB 1171.995972 3261.164062
SNP_A-4263484 AB 0.009995 AB 1867.005249 1555.051025
SNP_A-1978185 AA 0.004331 AA 2028.821289 468.362061
SNP_A-4264431 AB 0.002833 AB 1072.585327 814.715576
SNP_A-1980898 AA 0.000944 AA 1144.900879 336.967041
SNP_A-1983139 AA 0.007043 AA 3589.090088 1066.238159
SNP_A-4265735 AA 0.001657 AA 2018.431274 714.625488
SNP_A-1995832 BB 0.003202 BB 800.983887 1738.269043
SNP_A-1995893 BB 0.002461 BB 627.778687 2576.914062
SNP_A-1997689 BB 0.006036 BB 1039.449463 4013.871094
SNP_A-1997709 AA 0.002312 AA 1830.342285 406.667908
SNP_A-1997896 AB 0.003569 AB 1192.858521 1418.895630
SNP_A-1997922 NC 0.157730 AB 748.533264 499.882904
SNP_A-2000230 AA 0.003026 AA 2412.957031 1569.395142
SNP_A-2000332 AA 0.007854 AA 2972.391602 1137.665771
SNP_A-2000337 AA 0.002018 AA 1441.167725 335.009552
SNP_A-2000342 AA 0.033003 AA 2989.299072 1315.692627
SNP_A-4268173 AB 0.001734 AB 925.473938 889.930908

Total number of rows: 909622

Table truncated, full table size 46140 Kbytes.




Supplementary file Size Download File type/resource
GSM1636622_5345R_GenomeWideSNP_6_.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM1636622_5345R_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.2 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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