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Sample GSM1636661 Query DataSets for GSM1636661
Status Public on Feb 01, 2016
Title blood-MTC_2118R
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 0.010280 BB 856.711975 3286.881104
SNP_A-1967418 BB 0.004701 BB 385.030182 888.526306
SNP_A-1969580 BB 0.009932 BB 1542.292236 4837.079590
SNP_A-4263484 BB 0.002467 BB 504.703674 1766.067627
SNP_A-1978185 AA 0.000844 AA 1649.645020 429.351990
SNP_A-4264431 AB 0.004778 AB 1533.127197 1065.572388
SNP_A-1980898 BB 0.007426 BB 345.392548 1103.376221
SNP_A-1983139 AA 0.006967 AA 3440.754395 1074.009033
SNP_A-4265735 BB 0.002805 BB 873.325745 2012.607788
SNP_A-1995832 BB 0.011762 BB 835.037231 2762.602051
SNP_A-1995893 BB 0.001616 BB 541.441956 2610.043213
SNP_A-1997689 BB 0.003679 BB 751.011597 2875.718750
SNP_A-1997709 AA 0.004970 AA 1087.467896 306.346069
SNP_A-1997896 AB 0.015244 AB 1484.243530 1394.683228
SNP_A-1997922 AB 0.001191 AB 576.309875 570.703674
SNP_A-2000230 AA 0.000745 AA 2246.071533 1231.082275
SNP_A-2000332 AB 0.001097 AB 2443.546143 2685.708984
SNP_A-2000337 AA 0.012574 AA 913.018188 382.793488
SNP_A-2000342 AA 0.003740 AA 3689.199951 1061.035889
SNP_A-4268173 AA 0.005228 AA 2037.785278 454.001984

Total number of rows: 909622

Table truncated, full table size 46156 Kbytes.




Supplementary file Size Download File type/resource
GSM1636661_2118R_GenomeWideSNP_6_.CEL.gz 28.0 Mb (ftp)(http) CEL
GSM1636661_2118R_GenomeWideSNP_6_.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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