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Sample GSM463250 Query DataSets for GSM463250
Status Public on May 17, 2010
Title CHM062
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 0.008251233 AA 4053.938 786.2716
SNP_A-1967418 BB 0.001592368 BB 291.803 896.1244
SNP_A-1969580 BB 0.010886 BB 1509.361 5656.916
SNP_A-4263484 AA 0.001784308 AA 2513.725 414.7827
SNP_A-1978185 AA 0.00155755 AA 1739.459 364.882
SNP_A-4264431 AA 0.01315563 AA 2312.027 293.2523
SNP_A-1980898 BB 0.005565469 BB 308.1003 847.2802
SNP_A-1983139 AA 0.006843319 AA 2223.943 613.1563
SNP_A-4265735 AA 0.008808207 AA 1563.553 438.4248
SNP_A-1995832 BB 0.003641506 BB 584.4966 1988.925
SNP_A-1995893 BB 0.003954328 BB 464.181 2243.869
SNP_A-1997689 BB 0.01444865 BB 717.3389 3327.769
SNP_A-1997709 AA 0.003860529 AA 1498.512 237.4165
SNP_A-1997896 AA 0.0008718385 AA 1648.889 469.8318
SNP_A-1997922 BB 0.01044604 BB 488.0978 935.6109
SNP_A-2000230 AA 0.00303076 AA 3240.111 1188.031
SNP_A-2000332 AA 0.005316434 AA 3065.881 727.5497
SNP_A-2000337 AA 0.0008106813 AA 2038.691 329.4659
SNP_A-2000342 AA 0.009072284 AA 3245.753 765.3918
SNP_A-4268173 AA 0.00237465 AA 1937.477 310.6552

Total number of rows: 909622

Table truncated, full table size 44072 Kbytes.

Supplementary file Size Download File type/resource
GSM463250_071217CHM062.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM463250_071217CHM062.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463250_071217CHM062.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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