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Sample GSM463279 Query DataSets for GSM463279
Status Public on May 17, 2010
Title CHM097
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 0.02621734 AA 3330.39 1087.653
SNP_A-1967418 BB 8.467399E-05 BB 294.5418 848.1243
SNP_A-1969580 BB 0.001919743 BB 1224.64 4330.683
SNP_A-4263484 AA 0.01949879 AA 2384.412 647.5322
SNP_A-1978185 BB 0.002027177 BB 881.1955 3323.209
SNP_A-4264431 BB 0.005017442 BB 407.7834 1606.23
SNP_A-1980898 BB 0.003995642 BB 236.8185 777.3666
SNP_A-1983139 AA 0.002246325 AA 2745.325 653.2169
SNP_A-4265735 BB 0.002076401 BB 519.2126 1641.689
SNP_A-1995832 BB 0.001911376 BB 553.4445 1848.042
SNP_A-1995893 BB 0.00627638 BB 620.848 2550.013
SNP_A-1997689 BB 0.005402592 BB 1071.72 4532.298
SNP_A-1997709 AA 0.003008157 AA 1662.074 293.2413
SNP_A-1997896 AA 0.001207272 AA 1462.971 464.5466
SNP_A-1997922 BB 0.00433212 BB 481.2138 1353.901
SNP_A-2000230 AA 0.00156043 AA 3558.291 1418.521
SNP_A-2000332 AA 0.002733207 AA 3096.669 822.9156
SNP_A-2000337 AA 0.001239173 AA 1927.163 307.7104
SNP_A-2000342 AA 0.00897276 AA 3495.131 1150.635
SNP_A-4268173 BB 0.01698071 BB 350.5348 1174.429

Total number of rows: 909622

Table truncated, full table size 44037 Kbytes.




Supplementary file Size Download File type/resource
GSM463279_071219CHM097.CEL.gz 31.8 Mb (ftp)(http) CEL
GSM463279_071219CHM097.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463279_071219CHM097.birdseed-v2.chp.txt.gz 15.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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