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Sample GSM1637325 Query DataSets for GSM1637325
Status Public on Feb 01, 2016
Title blood-PTC_E11196
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 0.006680 BB 524.092712 3675.450684
SNP_A-1967418 AB 0.039939 AB 828.477478 730.242920
SNP_A-1969580 BB 0.002416 BB 900.181885 3283.608887
SNP_A-4263484 BB 0.007344 BB 667.300232 2386.480713
SNP_A-1978185 AA 0.005482 AA 1057.358398 353.313324
SNP_A-4264431 AA 0.021977 AA 2622.418213 329.592499
SNP_A-1980898 BB 0.008516 BB 277.838867 1157.086914
SNP_A-1983139 AA 0.006344 AA 3626.890137 834.556396
SNP_A-4265735 AA 0.077385 AA 5036.454590 700.310059
SNP_A-1995832 AB 0.005023 AB 1244.964355 903.267639
SNP_A-1995893 AB 0.000359 AB 1535.743164 1861.069946
SNP_A-1997689 BB 0.003432 BB 748.285278 3297.998291
SNP_A-1997709 AA 0.002757 AA 1586.821411 293.609467
SNP_A-1997896 AB 0.005076 AB 1180.372314 1397.802124
SNP_A-1997922 AA 0.004514 AA 898.597839 284.821442
SNP_A-2000230 AA 0.028137 AA 3687.529297 1269.893799
SNP_A-2000332 AB 0.013709 AB 3277.195801 3060.735352
SNP_A-2000337 AA 0.019437 AA 926.739319 260.539612
SNP_A-2000342 AA 0.017829 AA 4730.101074 913.875854
SNP_A-4268173 AA 0.027430 AA 2394.656738 307.857574

Total number of rows: 909622

Table truncated, full table size 46146 Kbytes.




Supplementary file Size Download File type/resource
GSM1637325_E11196_GenomeWideSNP_6_.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM1637325_E11196_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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