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Sample GSM463219 Query DataSets for GSM463219
Status Public on May 17, 2010
Title CHM026
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 0.005756429 AA 3645.127 660.2798
SNP_A-1967418 BB 0.004749497 BB 236.7806 816.0768
SNP_A-1969580 BB 0.001241068 BB 1204.476 4568.884
SNP_A-4263484 BB 0.002878116 BB 506.743 1863.438
SNP_A-1978185 AA 0.0005621415 AA 1705.072 396.1204
SNP_A-4264431 AA 0.009009409 AA 1579.388 392.2434
SNP_A-1980898 BB 0.003704424 BB 251.8591 772.6799
SNP_A-1983139 AA 0.002945503 AA 2406.586 627.2095
SNP_A-4265735 BB 0.01160267 BB 571.287 1380.871
SNP_A-1995832 AA 0.002249539 AA 2162.956 544.7439
SNP_A-1995893 AA 0.0115092 AA 1921.872 1162.483
SNP_A-1997689 BB 0.002362393 BB 916.5132 4682.153
SNP_A-1997709 AA 0.003600901 AA 2281.107 329.2027
SNP_A-1997896 AA 0.003129774 AA 1336.919 491.7323
SNP_A-1997922 AA 0.01184259 AA 981.5833 326.5115
SNP_A-2000230 AA 0.00431567 AA 2924.533 1311.773
SNP_A-2000332 AA 0.0007629592 AA 3299.729 941.4886
SNP_A-2000337 AA 0.003197752 AA 1696.888 342.5012
SNP_A-2000342 AA 0.00430056 AA 3396.035 859.5912
SNP_A-4268173 AA 0.001658548 AA 1761.061 330.516

Total number of rows: 909622

Table truncated, full table size 44187 Kbytes.




Supplementary file Size Download File type/resource
GSM463219_071218CHM026.CEL.gz 32.3 Mb (ftp)(http) CEL
GSM463219_071218CHM026.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463219_071218CHM026.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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