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Sample GSM463253 Query DataSets for GSM463253
Status Public on May 17, 2010
Title CHM065
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
E-mail(s) hayashi.kenshi@gmail.com
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
ID_REF
VALUE Call
Confidence
Forced Call
Signal A
Signal B

Data table
ID_REF VALUE Confidence Forced Call Signal A Signal B
SNP_A-2131660 BB 0.00877121 BB 1449.611 4043.727
SNP_A-1967418 BB 0.008403379 BB 322.0608 1021.263
SNP_A-1969580 BB 0.004965178 BB 1364.448 5201.883
SNP_A-4263484 BB 0.008052384 BB 520.485 1663.642
SNP_A-1978185 AA 0.0003778747 AA 1757.126 401.7482
SNP_A-4264431 BB 0.003627525 BB 446.8802 1626.792
SNP_A-1980898 BB 0.0002784536 BB 258.3655 891.365
SNP_A-1983139 BB 0.009101594 BB 699.866 1958.936
SNP_A-4265735 BB 0.003705138 BB 556.0917 1654.625
SNP_A-1995832 BB 0.01168894 BB 657.7643 2329.05
SNP_A-1995893 BB 0.002282331 BB 513.4077 2681.549
SNP_A-1997689 BB 0.002498474 BB 979.265 4355.776
SNP_A-1997709 AA 0.002621613 AA 1982.616 252.6075
SNP_A-1997896 AA 0.005885136 AA 1310.495 390.9516
SNP_A-1997922 BB 0.0009141324 BB 515.1715 1192.675
SNP_A-2000230 AA 0.001193112 AA 3438.764 1464.156
SNP_A-2000332 AA 0.001975224 AA 3177.56 938.8402
SNP_A-2000337 AA 0.001769657 AA 2079.867 350.2097
SNP_A-2000342 AA 0.00313763 AA 3446.973 980.7764
SNP_A-4268173 AA 0.004671408 AA 1593.547 311.5897

Total number of rows: 909622

Table truncated, full table size 44054 Kbytes.




Supplementary file Size Download File type/resource
GSM463253_071217CHM065.CEL.gz 31.0 Mb (ftp)(http) CEL
GSM463253_071217CHM065.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463253_071217CHM065.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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