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Sample GSM463210 Query DataSets for GSM463210
Status Public on May 17, 2010
Title CHM015
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 0.001616078 AA 3075.676 650.4469
SNP_A-1967418 BB 0.004837943 BB 266.8192 725.5102
SNP_A-1969580 BB 0.003292782 BB 1389.083 5103.421
SNP_A-4263484 BB 0.005055405 BB 470.1183 1814.047
SNP_A-1978185 AA 0.01730363 AA 2250.912 435.4745
SNP_A-4264431 AA 0.00798657 AA 1689.426 419.4789
SNP_A-1980898 BB 0.03990804 BB 340.6484 500.3145
SNP_A-1983139 AA 0.00687892 AA 2432.082 827.9263
SNP_A-4265735 BB 0.002232528 BB 518.5687 1654.924
SNP_A-1995832 AA 0.0050843 AA 2535.171 463.016
SNP_A-1995893 AA 0.01344163 AA 1837.043 1104.408
SNP_A-1997689 BB 0.01162592 BB 718.8042 3450.876
SNP_A-1997709 AA 0.007065834 AA 2508.755 297.5047
SNP_A-1997896 AA 0.01410523 AA 1376.303 654.7336
SNP_A-1997922 AA 0.007670353 AA 1422.781 330.4053
SNP_A-2000230 AA 0.002552812 AA 3531.553 1294.299
SNP_A-2000332 AA 0.0032568 AA 3553.826 955.8176
SNP_A-2000337 AA 0.01129882 AA 1495.91 277.4258
SNP_A-2000342 AA 0.002504548 AA 3525.387 898.3269
SNP_A-4268173 AA 0.002780623 AA 1710.13 333.5753

Total number of rows: 909622

Table truncated, full table size 43897 Kbytes.

Supplementary file Size Download File type/resource
GSM463210_071218CHM015.CEL.gz 31.2 Mb (ftp)(http) CEL
GSM463210_071218CHM015.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463210_071218CHM015.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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