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Sample GSM463275 Query DataSets for GSM463275
Status Public on May 17, 2010
Title CHM090
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 0.002269341 AA 3705.839 800.2795
SNP_A-1967418 BB 0.006364167 BB 361.0847 821.7501
SNP_A-1969580 BB 0.002516052 BB 1232.495 4812.609
SNP_A-4263484 AA 0.004542655 AA 2848.2 372.2188
SNP_A-1978185 AA 0.00372582 AA 1871.455 514.1422
SNP_A-4264431 BB 0.002413884 BB 431.2979 1460.924
SNP_A-1980898 BB 0.002239923 BB 227.5184 868.0412
SNP_A-1983139 AA 0.002625304 AA 2425.718 629.9381
SNP_A-4265735 AA 0.01312995 AA 1539.3 629.9381
SNP_A-1995832 BB 0.002209624 BB 623.9034 1887.913
SNP_A-1995893 BB 0.001079215 BB 469.3221 2588.624
SNP_A-1997689 BB 0.005253561 BB 928.851 4943.717
SNP_A-1997709 AA 0.006559009 AA 1345.799 269.9098
SNP_A-1997896 AA 0.003141314 AA 1335.035 456.778
SNP_A-1997922 BB 0.002329139 BB 555.6003 1360.995
SNP_A-2000230 AA 0.0009333393 AA 3273.195 1308.522
SNP_A-2000332 AA 0.001898119 AA 3134.977 870.6109
SNP_A-2000337 AA 0.006516274 AA 1751.483 437.7317
SNP_A-2000342 AA 0.002180307 AA 3728.094 872.1255
SNP_A-4268173 AA 0.003412939 AA 1617.496 296.2916

Total number of rows: 909622

Table truncated, full table size 44087 Kbytes.

Supplementary file Size Download File type/resource
GSM463275_071219CHM090.CEL.gz 30.7 Mb (ftp)(http) CEL
GSM463275_071219CHM090.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463275_071219CHM090.birdseed-v2.chp.txt.gz 15.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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