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Sample GSM463241 Query DataSets for GSM463241
Status Public on May 17, 2010
Title CHM053
Sample type genomic
 
Source name complete hydatidiform mole
Organism Homo sapiens
Characteristics tissue: complete hydatidiform mole
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from complete hydatidiform mole tissues using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen 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 washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.
Description none
Data processing CEL files were processed by Affymetrix Genotyping Console 3.0.1. Calls were generated using birdseed-v2 algorithm. Copy number analysis was performed using "Reference Model File Creation and Analysis" mode without with regional GC correction configuration.
 
Submission date Oct 20, 2009
Last update date May 17, 2010
Contact name Kenshi Hayashi
E-mail(s) hayashi.kenshi@gmail.com
Phone +81-92-642-6171
Organization name Kyushu University
Department Medical Institute of Bioregulation
Street address Maidashi 3-1-1, Higashi-ku
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
 
Platform ID GPL6801
Series (2)
GSE18642 Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles (Affymetrix)
GSE18701 Definitive SNP/CNV haplotype map of Asians determined using a collection of complete hydatidiform moles

Data table header descriptions
ID_REF
VALUE Call
Confidence
Forced Call
Signal A
Signal B

Data table
ID_REF VALUE Confidence Forced Call Signal A Signal B
SNP_A-2131660 AA 0.00964158 AA 4161.54 813.9448
SNP_A-1967418 BB 0.006600913 BB 356.6574 945.4511
SNP_A-1969580 BB 0.002162967 BB 1216.041 4298.162
SNP_A-4263484 AA 0.002842222 AA 2656.636 374.4898
SNP_A-1978185 AA 0.001371157 AA 1758.888 453.6316
SNP_A-4264431 AA 0.002624416 AA 1927.354 387.2906
SNP_A-1980898 BB 0.008675569 BB 324.1457 960.7125
SNP_A-1983139 AA 0.003446531 AA 2810.299 755.1389
SNP_A-4265735 AA 0.006870803 AA 1436.152 567.473
SNP_A-1995832 AA 0.02871376 AA 2970.937 404.0971
SNP_A-1995893 AA 0.00610479 AA 2648.168 1134.557
SNP_A-1997689 BB 0.0006458149 BB 849.1932 4442.36
SNP_A-1997709 AA 0.008744221 AA 2200.883 378.5851
SNP_A-1997896 AA 0.06049361 AA 442.2632 333.415
SNP_A-1997922 AB 0.05884773 AB 405.6787 242.9151
SNP_A-2000230 AA 0.005218624 AA 2863.453 1300.464
SNP_A-2000332 BB 0.003290024 BB 1198.801 3984.773
SNP_A-2000337 AA 0.006557181 AA 2118.083 416.4273
SNP_A-2000342 AA 0.0007507739 AA 3845.849 991.7269
SNP_A-4268173 AA 0.01409955 AA 2118.813 457.5889

Total number of rows: 909622

Table truncated, full table size 44141 Kbytes.




Supplementary file Size Download File type/resource
GSM463241_071219CHM053.CEL.gz 31.9 Mb (ftp)(http) CEL
GSM463241_071219CHM053.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463241_071219CHM053.birdseed-v2.chp.txt.gz 15.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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