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Sample GSM463211 Query DataSets for GSM463211
Status Public on May 17, 2010
Title CHM016
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 BB 0.01818365 BB 987.417 3013.486
SNP_A-1967418 BB 0.002071059 BB 278.846 782.3643
SNP_A-1969580 BB 0.004304856 BB 1234.361 4127.012
SNP_A-4263484 BB 0.001577375 BB 564.1934 1897.284
SNP_A-1978185 AA 0.002740809 AA 1753.595 342.4381
SNP_A-4264431 BB 0.01058091 BB 458.8783 1194.906
SNP_A-1980898 BB 0.007813581 BB 186.6178 858.1648
SNP_A-1983139 BB 0.009761229 BB 611.3295 1694.979
SNP_A-4265735 BB 0.002621154 BB 488.0444 1432.492
SNP_A-1995832 BB 0.003032244 BB 496.9279 1802.974
SNP_A-1995893 BB 0.01794205 BB 584.3981 3193.478
SNP_A-1997689 BB 0.002302143 BB 849.9438 4655.941
SNP_A-1997709 AA 0.002820896 AA 1687.855 237.2743
SNP_A-1997896 AA 0.002111017 AA 1542.598 421.1948
SNP_A-1997922 BB 0.001437852 BB 551.0664 1231.49
SNP_A-2000230 BB 0.01220493 BB 1039.13 3310.756
SNP_A-2000332 BB 0.005118656 BB 1406.034 3917.182
SNP_A-2000337 AA 0.004848308 AA 1674.885 303.2303
SNP_A-2000342 AA 0.001074652 AA 3976.443 937.3059
SNP_A-4268173 AA 0.01519709 AA 2291.657 389.3668

Total number of rows: 909622

Table truncated, full table size 44079 Kbytes.

Supplementary file Size Download File type/resource
GSM463211_071218CHM016.CEL.gz 31.5 Mb (ftp)(http) CEL
GSM463211_071218CHM016.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463211_071218CHM016.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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