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Sample GSM463231 Query DataSets for GSM463231
Status Public on May 17, 2010
Title CHM040
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 0.01510784 AA 3984.303 652.1998
SNP_A-1967418 BB 0.0202163 BB 228.2411 575.3234
SNP_A-1969580 BB 0.01133478 BB 825.881 4334.155
SNP_A-4263484 BB 0.01201673 BB 506.1349 1578.524
SNP_A-1978185 AA 0.006436891 AA 1461.799 285.8214
SNP_A-4264431 AA 0.004419636 AA 1719.254 383.1514
SNP_A-1980898 BB 0.0137838 BB 226.4775 629.3412
SNP_A-1983139 AA 0.004173973 AA 2848.397 648.0637
SNP_A-4265735 AA 0.008914314 AA 1060.462 303.3009
SNP_A-1995832 AA 0.02806775 AA 1662.589 441.5645
SNP_A-1995893 AA 0.001877802 AA 2182.156 1050.661
SNP_A-1997689 BB 0.003216983 BB 1002.251 4585.435
SNP_A-1997709 AA 0.001479755 AA 1985.676 308.7174
SNP_A-1997896 AA 0.008433623 AA 1152.022 408.4003
SNP_A-1997922 AA 0.005661232 AA 1001.492 242.7682
SNP_A-2000230 BB 0.008479225 BB 724.9729 3657.23
SNP_A-2000332 BB 0.01503526 BB 968.7246 4042.737
SNP_A-2000337 AA 0.0008284642 AA 1873.208 344.3777
SNP_A-2000342 AA 0.0163892 AA 3447.619 640.4119
SNP_A-4268173 AA 0.003067721 AA 1631.39 264.9886

Total number of rows: 909622

Table truncated, full table size 43923 Kbytes.

Supplementary file Size Download File type/resource
GSM463231_071218CHM040.CEL.gz 31.6 Mb (ftp)(http) CEL
GSM463231_071218CHM040.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463231_071218CHM040.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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