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Sample GSM1637340 Query DataSets for GSM1637340
Status Public on Feb 01, 2016
Title blood-PTC_E14181
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 AA 0.007091 AA 4049.926270 736.653992
SNP_A-1967418 BB 0.003158 BB 367.529449 724.498596
SNP_A-1969580 BB 0.007877 BB 697.653320 2767.619629
SNP_A-4263484 AB 0.004396 AB 1600.447144 1412.850708
SNP_A-1978185 AA 0.005684 AA 2006.388916 540.259705
SNP_A-4264431 AA 0.001881 AA 2157.107910 452.160431
SNP_A-1980898 AA 0.008638 AA 978.860596 357.357880
SNP_A-1983139 AA 0.000961 AA 2751.711914 722.026306
SNP_A-4265735 AA 0.001484 AA 2685.839355 778.981995
SNP_A-1995832 AA 0.004387 AA 2713.568604 719.612854
SNP_A-1995893 AA 0.003966 AA 2082.708008 1051.642700
SNP_A-1997689 BB 0.002674 BB 796.086609 3339.125732
SNP_A-1997709 AA 0.001646 AA 1567.865967 359.384796
SNP_A-1997896 AA 0.010367 AA 1466.988892 875.851624
SNP_A-1997922 AA 0.007991 AA 687.881042 321.301025
SNP_A-2000230 NC 0.574028 AA 2221.735840 1893.993530
SNP_A-2000332 AA 0.010066 AA 3265.075195 1393.577026
SNP_A-2000337 AA 0.007148 AA 1052.008423 379.521729
SNP_A-2000342 AA 0.002108 AA 3632.828857 1151.296631
SNP_A-4268173 BB 0.007267 BB 347.142090 971.349243

Total number of rows: 909622

Table truncated, full table size 46154 Kbytes.




Supplementary file Size Download File type/resource
GSM1637340_E14181_GenomeWideSNP_6_.CEL.gz 26.3 Mb (ftp)(http) CEL
GSM1637340_E14181_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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