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Sample GSM463242 Query DataSets for GSM463242
Status Public on May 17, 2010
Title CHM054
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 0.003355754 AA 3811.644 808.3195
SNP_A-1967418 BB 0.004730083 BB 237.1572 835.1974
SNP_A-1969580 BB 0.007829387 BB 1138.208 3817.545
SNP_A-4263484 AA 0.002246217 AA 2792.114 409.8134
SNP_A-1978185 AA 0.002045704 AA 1731.925 352.0559
SNP_A-4264431 BB 0.009734427 BB 430.1393 1220.534
SNP_A-1980898 BB 0.007364796 BB 224.5739 722.6147
SNP_A-1983139 AA 0.001367026 AA 2484.539 670.093
SNP_A-4265735 BB 0.00176585 BB 483.3129 1635.963
SNP_A-1995832 BB 0.002550822 BB 540.9254 1873.762
SNP_A-1995893 BB 0.007513487 BB 636.415 2537.274
SNP_A-1997689 BB 0.01042484 BB 1173.393 4549.283
SNP_A-1997709 AA 0.004312503 AA 1632.766 220.4361
SNP_A-1997896 AA 0.0001968748 AA 1553.392 470.5484
SNP_A-1997922 BB 0.0007910632 BB 495.5373 1236.203
SNP_A-2000230 AA 0.001241692 AA 3235.179 1402.394
SNP_A-2000332 BB 0.0004863079 BB 1199.638 3751.939
SNP_A-2000337 AA 0.001807368 AA 1845.317 371.3703
SNP_A-2000342 AA 0.003459228 AA 3389.627 949.7082
SNP_A-4268173 AA 0.00960412 AA 2030.59 431.4184

Total number of rows: 909622

Table truncated, full table size 44143 Kbytes.




Supplementary file Size Download File type/resource
GSM463242_071219CHM054.CEL.gz 32.0 Mb (ftp)(http) CEL
GSM463242_071219CHM054.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463242_071219CHM054.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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