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Sample GSM463244 Query DataSets for GSM463244
Status Public on May 17, 2010
Title CHM056
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 0.005509457 AA 3875.87 967.939
SNP_A-1967418 BB 0.001197922 BB 283.33 874.2791
SNP_A-1969580 BB 0.00650386 BB 1439.588 4306.314
SNP_A-4263484 AA 0.004199711 AA 2909.17 488.7255
SNP_A-1978185 AA 0.000672708 AA 1762.63 394.5048
SNP_A-4264431 BB 0.002610781 BB 519.788 1613.507
SNP_A-1980898 BB 0.01076019 BB 337.2907 861.1138
SNP_A-1983139 AA 0.002838719 AA 2703.096 774.138
SNP_A-4265735 BB 0.002678031 BB 476.0228 1665.931
SNP_A-1995832 BB 0.0008244063 BB 599.8412 1688.631
SNP_A-1995893 AA 0.002585029 AA 2171.222 998.1329
SNP_A-1997689 BB 0.006951774 BB 961.9661 3819.157
SNP_A-1997709 AA 0.009161524 AA 2615.486 365.101
SNP_A-1997896 AA 0.004341814 AA 1335.906 413.8142
SNP_A-1997922 AA 0.003159751 AA 1066.54 255.4135
SNP_A-2000230 AA 0.0008847794 AA 3372.271 1318.574
SNP_A-2000332 AA 0.006655047 AA 2887.109 816.7339
SNP_A-2000337 AA 0.003031003 AA 2004.157 271.5763
SNP_A-2000342 AA 0.001443673 AA 3611.867 951.5496
SNP_A-4268173 AA 0.001559774 AA 1763.694 329.4775

Total number of rows: 909622

Table truncated, full table size 44110 Kbytes.

Supplementary file Size Download File type/resource
GSM463244_071219CHM056.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM463244_071219CHM056.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463244_071219CHM056.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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