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Sample GSM463249 Query DataSets for GSM463249
Status Public on May 17, 2010
Title CHM061
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 0.03547771 AA 4723.333 1373.004
SNP_A-1967418 BB 0.01100962 BB 378.7722 981.0625
SNP_A-1969580 BB 0.007285033 BB 1533.297 4461.587
SNP_A-4263484 BB 0.04675336 BB 614.885 2815.615
SNP_A-1978185 AA 0.04028124 AA 2569.689 622.785
SNP_A-4264431 AA 0.002045512 AA 2016.856 352.6234
SNP_A-1980898 BB 0.02139289 BB 306.761 1207.392
SNP_A-1983139 AA 0.02982145 AA 2776.81 1064.194
SNP_A-4265735 BB 0.05500007 BB 777.5629 2304.154
SNP_A-1995832 BB 0.01017907 BB 707.7458 2259.803
SNP_A-1995893 BB 0.02260278 BB 761.5085 3122.738
SNP_A-1997689 BB 0.01412662 BB 1002.62 5398.595
SNP_A-1997709 AA 0.01108337 AA 2094.744 204.3062
SNP_A-1997896 AA 0.001032607 AA 1506.954 497.0768
SNP_A-1997922 BB 0.02419548 BB 766.8922 1660.612
SNP_A-2000230 AA 0.01379091 AA 3464.521 1848.901
SNP_A-2000332 AA 0.002438128 AA 3244.792 989.0079
SNP_A-2000337 AA 0.003753949 AA 1940.369 404.529
SNP_A-2000342 AA 0.002882521 AA 3449.745 957.5209
SNP_A-4268173 AA 0.000464581 AA 1800.157 316.7835

Total number of rows: 909622

Table truncated, full table size 43850 Kbytes.




Supplementary file Size Download File type/resource
GSM463249_071220CHM061.CEL.gz 31.1 Mb (ftp)(http) CEL
GSM463249_071220CHM061.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463249_071220CHM061.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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