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Sample GSM463225 Query DataSets for GSM463225
Status Public on May 17, 2010
Title CHM033
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 0.001811949 AA 3553.782 731.2229
SNP_A-1967418 BB 0.003086648 BB 336.1533 879.8439
SNP_A-1969580 BB 0.005117286 BB 1273.912 4118.976
SNP_A-4263484 AA 0.007264766 AA 2284.646 364.9587
SNP_A-1978185 AA 0.00245475 AA 1897.811 470.4622
SNP_A-4264431 AA 0.006647708 AA 1628.376 278.7431
SNP_A-1980898 BB 0.003946801 BB 289.1333 813.6897
SNP_A-1983139 BB 0.002487703 BB 475.8636 1851.232
SNP_A-4265735 BB 0.0007310414 BB 492.7723 1561.817
SNP_A-1995832 BB 0.001924979 BB 571.0712 1527.743
SNP_A-1995893 BB 0.001909827 BB 441.2375 2337.698
SNP_A-1997689 BB 0.00223635 BB 960.8514 4579.137
SNP_A-1997709 AA 0.0046933 AA 1576.942 217.3707
SNP_A-1997896 AA 0.007644332 AA 1413.616 347.748
SNP_A-1997922 BB 0.005137542 BB 424.8196 1043.788
SNP_A-2000230 BB 0.002510686 BB 1029.078 4264.551
SNP_A-2000332 BB 0.001011454 BB 1252.436 3675.604
SNP_A-2000337 AA 0.0007580884 AA 1880.479 333.8582
SNP_A-2000342 AA 0.002931771 AA 3971.6 1064.445
SNP_A-4268173 AA 0.0005833027 AA 1822.928 321.0948

Total number of rows: 909622

Table truncated, full table size 44207 Kbytes.

Supplementary file Size Download File type/resource
GSM463225_071218CHM033.CEL.gz 32.6 Mb (ftp)(http) CEL
GSM463225_071218CHM033.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463225_071218CHM033.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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