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Sample GSM1637334 Query DataSets for GSM1637334
Status Public on Feb 01, 2016
Title blood-PTC_E11587
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 BB 0.002150 BB 821.736145 4293.957031
SNP_A-1967418 NC 0.216153 AB 481.087219 717.074097
SNP_A-1969580 BB 0.007449 BB 765.960205 2699.479248
SNP_A-4263484 BB 0.009178 BB 480.052399 2113.799072
SNP_A-1978185 AA 0.011269 AA 1922.662354 627.158386
SNP_A-4264431 AA 0.024020 AA 2821.614502 391.218353
SNP_A-1980898 AB 0.006820 AB 885.499878 595.519165
SNP_A-1983139 AA 0.007588 AA 2129.880859 490.242554
SNP_A-4265735 AB 0.010977 AB 2299.312256 2388.628906
SNP_A-1995832 AB 0.012414 AB 1877.853149 1077.604736
SNP_A-1995893 AB 0.007950 AB 1252.685425 1933.479126
SNP_A-1997689 BB 0.002447 BB 854.663635 4311.269043
SNP_A-1997709 NC 0.811053 AA 1146.786865 499.393921
SNP_A-1997896 AB 0.008044 AB 1133.867432 1758.054443
SNP_A-1997922 AB 0.008359 AB 471.934998 609.181641
SNP_A-2000230 AB 0.005862 AB 2687.841064 2726.565674
SNP_A-2000332 AB 0.003721 AB 2182.820801 2528.848877
SNP_A-2000337 AA 0.002174 AA 1526.573364 393.141754
SNP_A-2000342 AA 0.001500 AA 3756.987549 994.889465
SNP_A-4268173 AB 0.004482 AB 907.553528 640.853943

Total number of rows: 909622

Table truncated, full table size 46151 Kbytes.




Supplementary file Size Download File type/resource
GSM1637334_E11587_GenomeWideSNP_6_.CEL.gz 25.1 Mb (ftp)(http) CEL
GSM1637334_E11587_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.6 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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