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Sample GSM463218 Query DataSets for GSM463218
Status Public on May 17, 2010
Title CHM024
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 BB 0.001541343 BB 896.6495 3468.21
SNP_A-1967418 BB 0.003205011 BB 273.8887 755.9492
SNP_A-1969580 BB 0.004587077 BB 1207.534 4935.217
SNP_A-4263484 AA 0.007945292 AA 2303.237 527.7213
SNP_A-1978185 AA 0.006968427 AA 1488.028 433.8988
SNP_A-4264431 AA 0.001739152 AA 2005.196 343.4399
SNP_A-1980898 BB 0.004178697 BB 231.5285 780.8458
SNP_A-1983139 AA 0.001931701 AA 2464.835 640.9026
SNP_A-4265735 BB 0.00319749 BB 423.3242 1356.787
SNP_A-1995832 BB 0.03603809 BB 553.4481 698.7258
SNP_A-1995893 BB 0.01504768 BB 505.6432 1976.442
SNP_A-1997689 BB 0.007831926 BB 839.6738 3628.833
SNP_A-1997709 AA 0.005176956 AA 1384.619 235.2479
SNP_A-1997896 AA 0.009380925 AA 1641.735 625.8439
SNP_A-1997922 BB 0.008426003 BB 518.4435 994.0488
SNP_A-2000230 AA 0.007565379 AA 2734.794 1168.032
SNP_A-2000332 BB 0.003728487 BB 1065.839 3637.637
SNP_A-2000337 AA 0.006205045 AA 1911.693 238.8555
SNP_A-2000342 AA 0.00134509 AA 3635.81 966.8051
SNP_A-4268173 AA 0.0009643654 AA 1869.484 313.5061

Total number of rows: 909622

Table truncated, full table size 44099 Kbytes.

Supplementary file Size Download File type/resource
GSM463218_071218CHM024.CEL.gz 31.4 Mb (ftp)(http) CEL
GSM463218_071218CHM024.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463218_071218CHM024.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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