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Sample GSM463282 Query DataSets for GSM463282
Status Public on May 17, 2010
Title CHM100
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 0.002019222 AA 3526.25 837.1724
SNP_A-1967418 BB 0.006525673 BB 235.3448 738.2032
SNP_A-1969580 BB 0.001635202 BB 1323.16 4876.58
SNP_A-4263484 BB 0.00701725 BB 636.669 2278.598
SNP_A-1978185 AA 0.005128622 AA 1675.182 500.3049
SNP_A-4264431 BB 0.01203818 BB 613.685 1292.07
SNP_A-1980898 BB 0.0008236556 BB 255.9663 932.1155
SNP_A-1983139 AA 0.003827312 AA 2339.37 679.633
SNP_A-4265735 AA 0.009819561 AA 1609.667 560.0496
SNP_A-1995832 BB 0.01311649 BB 528.5121 2277.318
SNP_A-1995893 BB 0.005025298 BB 548.6919 2826.891
SNP_A-1997689 BB 0.006798432 BB 820.5333 4981.391
SNP_A-1997709 AA 0.002956767 AA 1605.914 280.6749
SNP_A-1997896 AA 0.008791318 AA 1743.769 612.1636
SNP_A-1997922 BB 0.002026064 BB 569.7014 1331.055
SNP_A-2000230 AA 0.006858513 AA 2817.245 1121.394
SNP_A-2000332 BB 0.001436206 BB 1213.233 3579.627
SNP_A-2000337 AA 0.01976609 AA 1432.114 229.8451
SNP_A-2000342 AA 0.0003574443 AA 3847.3 974.5225
SNP_A-4268173 AA 0.002640799 AA 1889.243 280.6749

Total number of rows: 909622

Table truncated, full table size 44118 Kbytes.




Supplementary file Size Download File type/resource
GSM463282_071219CHM100.CEL.gz 31.3 Mb (ftp)(http) CEL
GSM463282_071219CHM100.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463282_071219CHM100.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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