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Sample GSM463233 Query DataSets for GSM463233
Status Public on May 17, 2010
Title CHM042
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 0.01377307 AA 2950.841 875.3951
SNP_A-1967418 BB 0.002298772 BB 274.5428 779.8674
SNP_A-1969580 BB 0.004866733 BB 1350.532 4247.637
SNP_A-4263484 BB 0.01012361 BB 710.8072 2250.173
SNP_A-1978185 BB 0.004956081 BB 1129.757 3728.92
SNP_A-4264431 BB 0.01247343 BB 427.262 1175.536
SNP_A-1980898 BB 0.002288414 BB 242.8225 818.2969
SNP_A-1983139 AA 0.01513975 AA 3071.935 892.5198
SNP_A-4265735 AA 0.00506658 AA 1203.347 318.965
SNP_A-1995832 AA 0.006723046 AA 1856.207 422.2798
SNP_A-1995893 AA 0.00632466 AA 2360.022 1323.445
SNP_A-1997689 BB 0.002099545 BB 790.8045 4500.02
SNP_A-1997709 AA 0.014507 AA 2834.846 313.2816
SNP_A-1997896 AA 0.01102628 AA 1083.515 396.6689
SNP_A-1997922 AA 0.004758825 AA 1221.697 374.0446
SNP_A-2000230 AA 0.003837596 AA 3451.228 1199.39
SNP_A-2000332 AA 0.01380272 AA 3835.001 1173.818
SNP_A-2000337 AA 0.005324686 AA 2097.505 240.8749
SNP_A-2000342 AA 0.008430283 AA 4083.457 1178.161
SNP_A-4268173 AA 0.001031826 AA 1743.042 310.4606

Total number of rows: 909622

Table truncated, full table size 44048 Kbytes.

Supplementary file Size Download File type/resource
GSM463233_071218CHM042.CEL.gz 32.7 Mb (ftp)(http) CEL
GSM463233_071218CHM042.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463233_071218CHM042.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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