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Sample GSM463234 Query DataSets for GSM463234
Status Public on May 17, 2010
Title CHM043
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 0.007033143 AA 2781.019 710.424
SNP_A-1967418 BB 0.003705726 BB 287.8784 740.9192
SNP_A-1969580 BB 0.02354721 BB 1897.225 4743.302
SNP_A-4263484 AA 0.001361884 AA 2651.622 479.5985
SNP_A-1978185 AA 0.001176319 AA 1762.894 449.3566
SNP_A-4264431 AA 0.004150299 AA 1677.238 354.7702
SNP_A-1980898 BB 0.002395951 BB 280.6291 850.0402
SNP_A-1983139 AA 0.001532972 AA 2715.144 669.5649
SNP_A-4265735 BB 0.009427903 BB 410.308 1179.391
SNP_A-1995832 AA 0.004908054 AA 2533.156 469.8161
SNP_A-1995893 AA 0.004336096 AA 2252.53 929.2436
SNP_A-1997689 BB 0.004526251 BB 795.7495 3849.752
SNP_A-1997709 AA 0.005628593 AA 2459.278 308.5812
SNP_A-1997896 AA 0.002750382 AA 1570.616 408.2528
SNP_A-1997922 AA 0.009585204 AA 946.8213 268.0544
SNP_A-2000230 AA 0.003410794 AA 3024.297 1216.641
SNP_A-2000332 AA 0.004545409 AA 3400.059 775.7841
SNP_A-2000337 AA 0.004847311 AA 2025.984 246.6041
SNP_A-2000342 AA 0.009776875 AA 2986.337 984.3538
SNP_A-4268173 AA 0.00251781 AA 1879.877 357.5539

Total number of rows: 909622

Table truncated, full table size 44055 Kbytes.

Supplementary file Size Download File type/resource
GSM463234_071218CHM043.CEL.gz 33.0 Mb (ftp)(http) CEL
GSM463234_071218CHM043.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463234_071218CHM043.birdseed-v2.chp.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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