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Sample GSM1637335 Query DataSets for GSM1637335
Status Public on Feb 01, 2016
Title blood-PTC_E11770
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 AB 0.002924 AB 3418.529541 3657.396973
SNP_A-1967418 BB 0.003153 BB 379.523407 812.457581
SNP_A-1969580 BB 0.007798 BB 699.487244 2774.217529
SNP_A-4263484 BB 0.001413 BB 670.317627 2062.575684
SNP_A-1978185 AA 0.015877 AA 2397.162354 431.053894
SNP_A-4264431 AB 0.005178 AB 1507.703857 1242.207153
SNP_A-1980898 NC 0.311081 AB 1115.146240 614.170715
SNP_A-1983139 AA 0.004535 AA 2468.549805 743.164917
SNP_A-4265735 AA 0.006101 AA 2921.650879 571.504883
SNP_A-1995832 AB 0.032035 AB 1454.586914 716.962952
SNP_A-1995893 AB 0.006382 AB 1543.102905 2209.524414
SNP_A-1997689 BB 0.005996 BB 935.794983 4642.533691
SNP_A-1997709 AA 0.004148 AA 1729.386475 287.401917
SNP_A-1997896 AA 0.005044 AA 1532.123413 506.852509
SNP_A-1997922 AB 0.017159 AB 940.002197 777.930481
SNP_A-2000230 AA 0.003033 AA 2308.366211 1212.980713
SNP_A-2000332 AA 0.009287 AA 3601.621582 1453.997925
SNP_A-2000337 AA 0.003735 AA 1226.891846 447.026123
SNP_A-2000342 AA 0.010553 AA 4583.138672 1086.111206
SNP_A-4268173 AA 0.005088 AA 1479.202759 222.987503

Total number of rows: 909622

Table truncated, full table size 46148 Kbytes.




Supplementary file Size Download File type/resource
GSM1637335_E11770_GenomeWideSNP_6_.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM1637335_E11770_GenomeWideSNP_6_.birdseed-v2.chp.gz 12.6 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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