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Sample GSM463248 Query DataSets for GSM463248
Status Public on May 17, 2010
Title CHM060
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 0.007715381 AA 3503.636 956.8914
SNP_A-1967418 BB 0.004185165 BB 242.2768 806.6982
SNP_A-1969580 BB 0.001896047 BB 1403.617 4972.397
SNP_A-4263484 AA 0.006291197 AA 2325.503 506.7095
SNP_A-1978185 AA 0.001183138 AA 1834.384 426.645
SNP_A-4264431 BB 0.002643656 BB 425.0533 1475.945
SNP_A-1980898 BB 0.01067903 BB 337.0246 863.5421
SNP_A-1983139 BB 0.001122638 BB 476.6127 1942.118
SNP_A-4265735 BB 0.002219295 BB 525.9316 1634.573
SNP_A-1995832 AA 0.00140631 AA 2216.997 410.8055
SNP_A-1995893 AA 0.0008629237 AA 2279.947 1127.502
SNP_A-1997689 BB 0.004755431 BB 971.3104 4007.438
SNP_A-1997709 AA 0.005239016 AA 2445.616 324.8834
SNP_A-1997896 AA 0.003217072 AA 1378.63 426.645
SNP_A-1997922 AA 0.001529633 AA 1149.421 255.5883
SNP_A-2000230 AA 0.001001771 AA 3381.244 1314.022
SNP_A-2000332 AA 0.0031186 AA 3200.994 776.551
SNP_A-2000337 AA 0.005315162 AA 1840.319 426.645
SNP_A-2000342 AA 0.005392037 AA 3359.171 831.2809
SNP_A-4268173 AA 0.0008119937 AA 1796.66 323.1772

Total number of rows: 909622

Table truncated, full table size 44130 Kbytes.

Supplementary file Size Download File type/resource
GSM463248_071217CHM060.CEL.gz 31.5 Mb (ftp)(http) CEL
GSM463248_071217CHM060.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463248_071217CHM060.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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