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Sample GSM463227 Query DataSets for GSM463227
Status Public on May 17, 2010
Title CHM035
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 0.004331044 AA 3590.835 671.3363
SNP_A-1967418 AA 0.01341063 AA 1138.891 269.5993
SNP_A-1969580 BB 0.006391127 BB 1241.106 4001.147
SNP_A-4263484 AA 0.005194724 AA 2506.824 343.7511
SNP_A-1978185 AA 0.001959321 AA 1771.943 470.055
SNP_A-4264431 AA 0.004418515 AA 1750.031 274.6877
SNP_A-1980898 BB 0.003156458 BB 244.7381 790.5737
SNP_A-1983139 AA 0.003268005 AA 2724.78 607.2358
SNP_A-4265735 BB 0.006589388 BB 449.473 1267.716
SNP_A-1995832 AA 0.002391372 AA 2091.626 504.381
SNP_A-1995893 AA 0.005844956 AA 2182.881 885.2715
SNP_A-1997689 BB 0.001806221 BB 834.4437 4108.717
SNP_A-1997709 AA 0.0007374707 AA 1826.143 268.3819
SNP_A-1997896 AA 0.002920597 AA 1776.755 503.4545
SNP_A-1997922 AA 0.001688808 AA 1200.187 259.868
SNP_A-2000230 AA 0.006207504 AA 2813.12 1317.046
SNP_A-2000332 AA 0.003284164 AA 3046.198 852.3506
SNP_A-2000337 AA 0.0025786 AA 2150.242 294.0164
SNP_A-2000342 AA 0.007385345 AA 3473.06 762.9277
SNP_A-4268173 AA 0.003686259 AA 1720.642 349.808

Total number of rows: 909622

Table truncated, full table size 44055 Kbytes.

Supplementary file Size Download File type/resource
GSM463227_071218CHM035.CEL.gz 32.5 Mb (ftp)(http) CEL
GSM463227_071218CHM035.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463227_071218CHM035.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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