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Sample GSM1637336 Query DataSets for GSM1637336
Status Public on Feb 01, 2016
Title blood-PTC_E11771
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: PTC
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 0.000772 AB 3433.498779 3185.014648
SNP_A-1967418 BB 0.005838 BB 270.808350 774.579224
SNP_A-1969580 BB 0.011950 BB 617.555359 2468.686523
SNP_A-4263484 BB 0.004071 BB 641.029297 2226.416992
SNP_A-1978185 AA 0.004719 AA 1938.059448 433.730072
SNP_A-4264431 AA 0.004768 AA 2201.343506 387.513245
SNP_A-1980898 BB 0.012281 BB 306.206665 1240.307007
SNP_A-1983139 AA 0.003338 AA 2666.900879 589.269226
SNP_A-4265735 AA 0.001821 AA 2796.536133 775.805603
SNP_A-1995832 AA 0.001876 AA 2510.205811 658.884460
SNP_A-1995893 AA 0.021780 AA 2189.666260 1507.057617
SNP_A-1997689 BB 0.003145 BB 705.234314 3618.562988
SNP_A-1997709 AA 0.001359 AA 1700.194458 366.798004
SNP_A-1997896 AA 0.003199 AA 1307.106079 718.145081
SNP_A-1997922 AA 0.002866 AA 851.601929 298.179718
SNP_A-2000230 AB 0.090844 AB 2481.037109 2147.110107
SNP_A-2000332 AB 0.004197 AB 2447.899414 2349.142822
SNP_A-2000337 AA 0.001117 AA 1305.206421 400.386536
SNP_A-2000342 AA 0.001701 AA 3775.380127 988.416931
SNP_A-4268173 AA 0.001371 AA 1646.693237 332.875885

Total number of rows: 909622

Table truncated, full table size 46142 Kbytes.




Supplementary file Size Download File type/resource
GSM1637336_E11771_GenomeWideSNP_6_.CEL.gz 26.4 Mb (ftp)(http) CEL
GSM1637336_E11771_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.8 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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