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Sample GSM1636601 Query DataSets for GSM1636601
Status Public on Feb 01, 2016
Title blood-MTC_9620
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics phenotype: MTC
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 0.003718 BB 1294.042236 5543.950684
SNP_A-1967418 BB 0.000870 BB 356.034241 766.375549
SNP_A-1969580 BB 0.002209 BB 1066.845947 4179.434082
SNP_A-4263484 BB 0.006247 BB 432.775574 1411.843994
SNP_A-1978185 AA 0.003218 AA 1199.370605 429.476776
SNP_A-4264431 AA 0.000692 AA 1836.561279 411.469452
SNP_A-1980898 AA 0.003858 AA 1044.010132 366.732849
SNP_A-1983139 AA 0.009596 AA 2091.402832 619.027100
SNP_A-4265735 AA 0.006138 AA 1599.086182 667.613464
SNP_A-1995832 AB 0.007189 AB 1409.940308 1569.781006
SNP_A-1995893 AB 0.007672 AB 1886.535156 1795.562500
SNP_A-1997689 BB 0.004970 BB 669.400818 2758.567383
SNP_A-1997709 AA 0.002941 AA 2167.826416 415.794586
SNP_A-1997896 AB 0.001278 AB 936.096130 1362.760010
SNP_A-1997922 AA 0.015035 AA 614.597656 310.831848
SNP_A-2000230 AA 0.007994 AA 2215.582520 796.863831
SNP_A-2000332 AB 0.014402 AB 3319.325439 3243.837402
SNP_A-2000337 AA 0.006719 AA 1724.947632 360.361908
SNP_A-2000342 AA 0.006398 AA 3110.514160 687.036804
SNP_A-4268173 AA 0.001278 AA 1516.606445 366.732849

Total number of rows: 909622

Table truncated, full table size 46136 Kbytes.




Supplementary file Size Download File type/resource
GSM1636601_9620_GenomeWideSNP_6_.CEL.gz 27.1 Mb (ftp)(http) CEL
GSM1636601_9620_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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