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Sample GSM1636658 Query DataSets for GSM1636658
Status Public on Feb 01, 2016
Title blood-MTC_2237R
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 0.014922 AB 2291.065918 1632.092163
SNP_A-1967418 BB 0.009912 BB 284.575745 556.824646
SNP_A-1969580 BB 0.004488 BB 1386.121948 4404.654785
SNP_A-4263484 BB 0.038319 BB 719.464172 1181.828247
SNP_A-1978185 AA 0.008100 AA 1675.292114 310.141968
SNP_A-4264431 AA 0.005793 AA 2090.320068 601.379700
SNP_A-1980898 BB 0.004463 BB 417.877411 957.464111
SNP_A-1983139 AA 0.005976 AA 2790.980469 927.616638
SNP_A-4265735 AA 0.007879 AA 1742.158325 774.747742
SNP_A-1995832 BB 0.000624 BB 798.112305 2027.816895
SNP_A-1995893 BB 0.009258 BB 621.813782 2117.670654
SNP_A-1997689 BB 0.008981 BB 619.241028 2343.711914
SNP_A-1997709 AA 0.007054 AA 951.368164 271.816437
SNP_A-1997896 AA 0.017878 AA 1885.367554 749.059021
SNP_A-1997922 AB 0.006873 AB 464.275299 539.965210
SNP_A-2000230 AA 0.084735 AA 1707.690308 1312.478760
SNP_A-2000332 AB 0.013699 AB 3132.039551 3348.958496
SNP_A-2000337 NC 0.717831 AB 1037.946655 631.051819
SNP_A-2000342 AA 0.007774 AA 2637.809082 994.529114
SNP_A-4268173 AA 0.014845 AA 2289.901855 384.374237

Total number of rows: 909622

Table truncated, full table size 46171 Kbytes.




Supplementary file Size Download File type/resource
GSM1636658_2237R_GenomeWideSNP_6_.CEL.gz 26.1 Mb (ftp)(http) CEL
GSM1636658_2237R_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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