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Sample GSM463280 Query DataSets for GSM463280
Status Public on May 17, 2010
Title CHM098
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 0.0007071014 AA 3453.28 774.799
SNP_A-1967418 BB 0.008986573 BB 372.462 793.2983
SNP_A-1969580 BB 0.003940624 BB 1135.281 4724.382
SNP_A-4263484 AA 0.003804606 AA 2516.092 515.1379
SNP_A-1978185 BB 0.005871015 BB 1146.368 3777.806
SNP_A-4264431 BB 0.003083683 BB 471.1946 1366.595
SNP_A-1980898 BB 0.01169882 BB 242.2944 641.999
SNP_A-1983139 AA 0.003502977 AA 2363.397 636.5854
SNP_A-4265735 BB 0.001923608 BB 510.293 1644.442
SNP_A-1995832 AA 0.002835812 AA 2298.866 597.2164
SNP_A-1995893 AA 0.005581163 AA 2106.999 1183.074
SNP_A-1997689 BB 0.01598374 BB 1248.411 4483.993
SNP_A-1997709 AA 0.005457819 AA 2409.02 344.4056
SNP_A-1997896 AA 0.002796379 AA 1429.332 526.1624
SNP_A-1997922 AA 0.00274797 AA 1300.464 342.2148
SNP_A-2000230 AA 0.008835378 AA 3606.74 1763.159
SNP_A-2000332 AA 0.03699884 AA 3321.793 1399.536
SNP_A-2000337 AA 0.04434747 AA 1260.25 598.7529
SNP_A-2000342 AA 0.009424443 AA 3516.24 1161.204
SNP_A-4268173 AA 0.00617838 AA 2014.794 397.7439

Total number of rows: 909622

Table truncated, full table size 43884 Kbytes.

Supplementary file Size Download File type/resource
GSM463280_071219CHM098.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM463280_071219CHM098.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463280_071219CHM098.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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