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Sample GSM1637315 Query DataSets for GSM1637315
Status Public on Feb 01, 2016
Title blood-PTC_E11029
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 0.010563 BB 634.474609 3154.700439
SNP_A-1967418 AB 0.001809 AB 591.396606 539.901062
SNP_A-1969580 BB 0.001770 BB 1119.828125 4116.323730
SNP_A-4263484 AB 0.013213 AB 1792.466431 1706.474854
SNP_A-1978185 AA 0.004177 AA 1196.447876 357.203003
SNP_A-4264431 AA 0.046342 AA 3109.762207 370.260010
SNP_A-1980898 BB 0.004196 BB 374.661530 860.769409
SNP_A-1983139 AA 0.009858 AA 1923.430298 549.217529
SNP_A-4265735 AB 0.001449 AB 1706.765503 1634.258545
SNP_A-1995832 AA 0.054265 AA 1604.440918 410.230927
SNP_A-1995893 AA 0.002737 AA 2365.980713 1268.151123
SNP_A-1997689 BB 0.010249 BB 1021.025879 4801.825684
SNP_A-1997709 AA 0.005794 AA 1588.037842 263.484985
SNP_A-1997896 AA 0.020196 AA 2006.494019 789.429016
SNP_A-1997922 AA 0.022356 AA 1276.798584 340.086700
SNP_A-2000230 AB 0.047850 AB 2609.775635 2223.571289
SNP_A-2000332 AB 0.002379 AB 2552.972656 2905.249268
SNP_A-2000337 AA 0.006487 AA 1557.693237 489.981842
SNP_A-2000342 AA 0.009100 AA 4504.053711 1094.133911
SNP_A-4268173 AA 0.004249 AA 1819.176758 396.781403

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.




Supplementary file Size Download File type/resource
GSM1637315_E11029_GenomeWideSNP_6_.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM1637315_E11029_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.7 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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