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Sample GSM463237 Query DataSets for GSM463237
Status Public on May 17, 2010
Title CHM048
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 0.007844084 AA 2755.67 715.824
SNP_A-1967418 BB 0.005133932 BB 240.0495 766.2616
SNP_A-1969580 BB 0.009781012 BB 1377.115 4030.993
SNP_A-4263484 AA 0.003038626 AA 2525.903 502.2196
SNP_A-1978185 AA 0.003696749 AA 1539.718 387.8828
SNP_A-4264431 BB 0.002537548 BB 436.7523 1428.595
SNP_A-1980898 BB 0.002675785 BB 228.4289 838.158
SNP_A-1983139 AA 0.0008467205 AA 2628.218 718.5314
SNP_A-4265735 AA 0.000543059 AA 1354.915 444.3046
SNP_A-1995832 AA 0.007488415 AA 1837.788 440.9536
SNP_A-1995893 AA 0.004093717 AA 2571.989 1128.931
SNP_A-1997689 BB 0.002520433 BB 888.1119 4059.105
SNP_A-1997709 AA 0.004654813 AA 1968.391 232.2943
SNP_A-1997896 AA 0.001530326 AA 1509.857 511.7952
SNP_A-1997922 AA 0.01072496 AA 950.8487 289.707
SNP_A-2000230 BB 0.004413852 BB 971.1519 3597.296
SNP_A-2000332 BB 0.002860602 BB 1126.435 3823.608
SNP_A-2000337 AA 0.003015686 AA 2183.485 292.2921
SNP_A-2000342 AA 0.00842981 AA 3186.483 1059.303
SNP_A-4268173 AA 0.001445473 AA 1874.553 336.9572

Total number of rows: 909622

Table truncated, full table size 44144 Kbytes.

Supplementary file Size Download File type/resource
GSM463237_071218CHM048.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM463237_071218CHM048.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463237_071218CHM048.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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