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Sample GSM463199 Query DataSets for GSM463199
Status Public on May 17, 2010
Title CHM003
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 AA 0.004590387 AA 3851.245 778.3211
SNP_A-1967418 BB 0.008814775 BB 344.5349 1011.051
SNP_A-1969580 BB 0.002776343 BB 1256.354 4881.851
SNP_A-4263484 BB 0.006043006 BB 653.111 2219.553
SNP_A-1978185 BB 0.002587124 BB 1060.951 3647.569
SNP_A-4264431 BB 0.002752722 BB 422.5794 1495.643
SNP_A-1980898 BB 0.006017542 BB 247.936 1069.664
SNP_A-1983139 BB 0.009341485 BB 585.0688 2389.236
SNP_A-4265735 BB 0.008697469 BB 394.9746 1684.132
SNP_A-1995832 AA 0.0006942793 AA 2291.17 465.3391
SNP_A-1995893 AA 0.010132 AA 2678.74 1392.246
SNP_A-1997689 BB 0.01374411 BB 918.7979 5386.144
SNP_A-1997709 AA 0.009830809 AA 2154.064 383.2711
SNP_A-1997896 AA 0.001218243 AA 1458.372 478.4172
SNP_A-1997922 AA 0.01019959 AA 1471.852 358.94
SNP_A-2000230 BB 0.00109308 BB 1082.659 4122.073
SNP_A-2000332 BB 0.002229851 BB 1318.816 3838.562
SNP_A-2000337 AA 0.005957645 AA 2012.964 424.4836
SNP_A-2000342 AA 0.001794331 AA 4100.063 977.4102
SNP_A-4268173 BB 0.003205961 BB 350.7032 1652.857

Total number of rows: 909622

Table truncated, full table size 44105 Kbytes.




Supplementary file Size Download File type/resource
GSM463199_071215CHM003.CEL.gz 31.1 Mb (ftp)(http) CEL
GSM463199_071215CHM003.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463199_071215CHM003.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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