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Sample GSM463220 Query DataSets for GSM463220
Status Public on May 17, 2010
Title CHM028
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 0.004631452 AA 2771.606 527.9559
SNP_A-1967418 BB 0.01952101 BB 252.049 566.9875
SNP_A-1969580 BB 0.005599832 BB 1087.067 4740.982
SNP_A-4263484 AA 0.002970753 AA 2585.188 373.2442
SNP_A-1978185 AA 0.006209807 AA 1821.769 307.3431
SNP_A-4264431 AA 0.001939313 AA 2007.981 327.224
SNP_A-1980898 BB 0.004913695 BB 209.9093 823.865
SNP_A-1983139 AA 0.01051876 AA 2959.249 557.9366
SNP_A-4265735 BB 0.00906228 BB 360.8979 1188.109
SNP_A-1995832 BB 0.01579821 BB 821.2097 1594.405
SNP_A-1995893 BB 0.002479969 BB 433.2697 2623.802
SNP_A-1997689 BB 0.01919131 BB 491.3191 3555.082
SNP_A-1997709 AA 0.003961687 AA 1479.393 261.8691
SNP_A-1997896 AA 0.00461382 AA 1818.177 416.7217
SNP_A-1997922 BB 0.01123203 BB 385.3913 905.3176
SNP_A-2000230 BB 0.008601261 BB 881.8231 3367.84
SNP_A-2000332 BB 0.003580668 BB 1261.671 3480.137
SNP_A-2000337 AA 0.006032335 AA 2291.775 254.4943
SNP_A-2000342 AA 0.007455567 AA 3441.062 765.1653
SNP_A-4268173 BB 0.004725061 BB 397.5829 1450.491

Total number of rows: 909622

Table truncated, full table size 43851 Kbytes.

Supplementary file Size Download File type/resource
GSM463220_071218CHM028.CEL.gz 31.1 Mb (ftp)(http) CEL
GSM463220_071218CHM028.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463220_071218CHM028.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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