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Sample GSM463216 Query DataSets for GSM463216
Status Public on May 17, 2010
Title CHM022
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 0.01027499 AA 4319.407 1057.024
SNP_A-1967418 BB 0.01588218 BB 365.0713 1072.59
SNP_A-1969580 BB 0.003885445 BB 1125.467 4085.034
SNP_A-4263484 BB 0.002054097 BB 501.8507 2051.045
SNP_A-1978185 AA 0.004917077 AA 2011.596 457.4254
SNP_A-4264431 AA 0.002324333 AA 1745.455 339.9109
SNP_A-1980898 BB 0.002034612 BB 267.2625 963.9753
SNP_A-1983139 AA 0.005319067 AA 2416.874 792.5852
SNP_A-4265735 AA 0.001563963 AA 1335.919 396.6527
SNP_A-1995832 AA 0.006900204 AA 1847.389 406.1163
SNP_A-1995893 AA 0.008292321 AA 2002.169 1164.885
SNP_A-1997689 BB 0.004113681 BB 1013.051 4713.876
SNP_A-1997709 AA 0.02054269 AA 2580.398 436.3612
SNP_A-1997896 AA 0.009751789 AA 1202.027 365.0713
SNP_A-1997922 AA 0.007922434 AA 1433.287 347.649
SNP_A-2000230 AA 0.01338452 AA 3240.511 1788.753
SNP_A-2000332 AA 0.006632175 AA 2996.107 980.9243
SNP_A-2000337 AA 0.001661565 AA 1832.041 365.0713
SNP_A-2000342 AA 0.002441435 AA 3726.801 1041.041
SNP_A-4268173 AA 0.008963825 AA 1464.222 213.3465

Total number of rows: 909622

Table truncated, full table size 44107 Kbytes.

Supplementary file Size Download File type/resource
GSM463216_071218CHM022.CEL.gz 31.6 Mb (ftp)(http) CEL
GSM463216_071218CHM022.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463216_071218CHM022.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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