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Sample GSM463243 Query DataSets for GSM463243
Status Public on May 17, 2010
Title CHM055
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 0.006221555 AA 3832.512 983.449
SNP_A-1967418 BB 0.00602668 BB 291.5583 700.9458
SNP_A-1969580 BB 0.05429911 BB 1427.03 3601.096
SNP_A-4263484 AA 0.003316572 AA 2799.229 504.9569
SNP_A-1978185 AA 0.00853437 AA 2028.616 581.5276
SNP_A-4264431 AA 0.01898365 AA 1336.84 334.6515
SNP_A-1980898 BB 0.001561913 BB 247.3009 837.637
SNP_A-1983139 AA 0.007313733 AA 2732.256 864.6125
SNP_A-4265735 BB 0.002479796 BB 487.1146 1668.648
SNP_A-1995832 AA 0.002186159 AA 2417.38 513.2475
SNP_A-1995893 AA 0.006628432 AA 2252.104 1294.211
SNP_A-1997689 BB 0.003098848 BB 984.8447 4652.542
SNP_A-1997709 AA 0.004153658 AA 2336.592 295.0113
SNP_A-1997896 AA 0.005084864 AA 1299.325 535.9894
SNP_A-1997922 AA 0.002930207 AA 1089.803 289.811
SNP_A-2000230 AA 0.01207659 AA 2815.912 1568.66
SNP_A-2000332 AA 0.03495591 AA 2692.24 1160.895
SNP_A-2000337 AA 0.006256687 AA 2284.708 370.9606
SNP_A-2000342 AA 0.007207872 AA 3422.257 1104.13
SNP_A-4268173 AA 0.01522828 AA 1659.692 423.5233

Total number of rows: 909622

Table truncated, full table size 44037 Kbytes.

Supplementary file Size Download File type/resource
GSM463243_071219CHM055.CEL.gz 33.0 Mb (ftp)(http) CEL
GSM463243_071219CHM055.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463243_071219CHM055.birdseed-v2.chp.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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