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Sample GSM463214 Query DataSets for GSM463214
Status Public on May 17, 2010
Title CHM020
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 0.001348878 AA 3589.927 791.5849
SNP_A-1967418 BB 0.01108543 BB 369.7363 1005.908
SNP_A-1969580 BB 0.001615746 BB 1388.521 4604.298
SNP_A-4263484 AA 0.003599976 AA 2911.258 438.306
SNP_A-1978185 AA 0.004083555 AA 1937.872 512.5085
SNP_A-4264431 AA 0.01234774 AA 2331.249 368.0378
SNP_A-1980898 BB 0.00243587 BB 224.5577 876.3641
SNP_A-1983139 AA 0.001483149 AA 2587.765 739.0331
SNP_A-4265735 BB 0.003654332 BB 551.9224 1680.846
SNP_A-1995832 BB 0.003253125 BB 653.0931 1938.084
SNP_A-1995893 BB 0.003136315 BB 470.1856 2713.229
SNP_A-1997689 BB 0.005503756 BB 1037.655 4818.244
SNP_A-1997709 AA 0.005004711 AA 1421.921 266.5824
SNP_A-1997896 AA 0.006075691 AA 1714.244 367.8457
SNP_A-1997922 BB 0.02353393 BB 402.4351 1507.896
SNP_A-2000230 AA 0.001937573 AA 3205.755 1433.568
SNP_A-2000332 AA 0.004377735 AA 3258.453 1047.923
SNP_A-2000337 AA 0.01033014 AA 1390.832 367.8457
SNP_A-2000342 AA 0.00121138 AA 4021.157 977.2424
SNP_A-4268173 AA 0.0006322446 AA 1848.24 311.9689

Total number of rows: 909622

Table truncated, full table size 44111 Kbytes.

Supplementary file Size Download File type/resource
GSM463214_071218CHM020.CEL.gz 30.9 Mb (ftp)(http) CEL
GSM463214_071218CHM020.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463214_071218CHM020.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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