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Sample GSM463235 Query DataSets for GSM463235
Status Public on May 17, 2010
Title CHM046
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
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
Forced Call
Signal A
Signal B

Data table
ID_REF VALUE Confidence Forced Call Signal A Signal B
SNP_A-2131660 AA 0.0002131258 AA 3323.063 728.7218
SNP_A-1967418 BB 0.007012152 BB 241.7908 935.9108
SNP_A-1969580 BB 0.001767891 BB 1323.62 4457.734
SNP_A-4263484 BB 0.003654193 BB 650.9138 1941.862
SNP_A-1978185 AA 0.003167716 AA 1659.86 460.0636
SNP_A-4264431 AA 0.003163057 AA 1712.616 348.9819
SNP_A-1980898 BB 0.001453305 BB 234.3655 890.0803
SNP_A-1983139 AA 0.002399181 AA 2784.205 699.441
SNP_A-4265735 AA 0.002826893 AA 1452 461.6522
SNP_A-1995832 AA 0.007124749 AA 2437.004 703.658
SNP_A-1995893 AA 0.003116596 AA 2430.849 1248.321
SNP_A-1997689 BB 0.001739976 BB 942.4619 4298.596
SNP_A-1997709 AA 0.004852756 AA 2351.462 342.411
SNP_A-1997896 AA 0.01036191 AA 1542.523 313.5798
SNP_A-1997922 AA 0.0028041 AA 1185.392 238.8
SNP_A-2000230 AA 0.006435791 AA 2803.154 1321.792
SNP_A-2000332 AA 0.0008954065 AA 3374.647 897.4995
SNP_A-2000337 AA 0.00423251 AA 1646.085 376.2245
SNP_A-2000342 AA 0.004102569 AA 3619.347 1072.03
SNP_A-4268173 AA 0.02673245 AA 2299.987 261.7654

Total number of rows: 909622

Table truncated, full table size 44119 Kbytes.

Supplementary file Size Download File type/resource
GSM463235_071218CHM046.CEL.gz 31.4 Mb (ftp)(http) CEL
GSM463235_071218CHM046.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463235_071218CHM046.birdseed-v2.chp.txt.gz 15.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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