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Sample GSM1636602 Query DataSets for GSM1636602
Status Public on Feb 01, 2016
Title blood-MTC_9512
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 0.001431 BB 1174.900635 4921.821289
SNP_A-1967418 BB 0.005515 BB 268.447937 683.638733
SNP_A-1969580 BB 0.001813 BB 988.630371 3678.436768
SNP_A-4263484 BB 0.003051 BB 589.958801 1591.909912
SNP_A-1978185 AA 0.002078 AA 1319.676270 445.193481
SNP_A-4264431 AA 0.004750 AA 2200.017578 427.738800
SNP_A-1980898 BB 0.006736 BB 356.722137 768.633362
SNP_A-1983139 AA 0.011159 AA 1989.505493 558.984009
SNP_A-4265735 AB 0.006497 AB 1036.497559 990.015991
SNP_A-1995832 AA 0.002349 AA 2470.633789 516.597534
SNP_A-1995893 AA 0.003176 AA 2658.784912 1057.012329
SNP_A-1997689 BB 0.006262 BB 619.283081 2688.234375
SNP_A-1997709 AA 0.003010 AA 1950.316650 421.673340
SNP_A-1997896 AA 0.001047 AA 1256.649780 556.893311
SNP_A-1997922 AA 0.006961 AA 673.970093 318.397064
SNP_A-2000230 AA 0.007932 AA 2041.746826 788.071167
SNP_A-2000332 AB 0.013970 AB 3317.515869 3225.072754
SNP_A-2000337 AA 0.001919 AA 1529.701782 387.034363
SNP_A-2000342 AA 0.003633 AA 2903.236328 886.628418
SNP_A-4268173 AA 0.001553 AA 1444.401123 284.311554

Total number of rows: 909622

Table truncated, full table size 46143 Kbytes.




Supplementary file Size Download File type/resource
GSM1636602_9512_GenomeWideSNP_6_.CEL.gz 27.1 Mb (ftp)(http) CEL
GSM1636602_9512_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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