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Sample GSM463217 Query DataSets for GSM463217
Status Public on May 17, 2010
Title CHM023
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 0.005825437 AA 4028.294 963.7895
SNP_A-1967418 AA 0.008648068 AA 794.0103 300.6833
SNP_A-1969580 BB 0.003053096 BB 1425.448 5109.292
SNP_A-4263484 BB 0.003561804 BB 589.9153 1816.18
SNP_A-1978185 AA 0.0008127944 AA 1807.625 433.3176
SNP_A-4264431 AA 0.002945973 AA 1909.074 392.4163
SNP_A-1980898 BB 0.004729899 BB 243.5114 753.2683
SNP_A-1983139 AA 0.00176325 AA 2711.237 733.9009
SNP_A-4265735 AA 0.00240348 AA 1340.433 382.1666
SNP_A-1995832 BB 0.0005063789 BB 562.515 1640.68
SNP_A-1995893 BB 0.00165425 BB 416.8127 2514.551
SNP_A-1997689 BB 0.005714505 BB 1057.772 4244.366
SNP_A-1997709 AA 0.004793793 AA 1767.176 218.4995
SNP_A-1997896 AA 0.003653995 AA 1425.137 543.553
SNP_A-1997922 BB 0.00864695 BB 471.1947 953.5518
SNP_A-2000230 AA 0.004024565 AA 3207.356 1537.975
SNP_A-2000332 AA 0.003331345 AA 3289.451 777.7317
SNP_A-2000337 AA 0.001927142 AA 1957.985 375.2492
SNP_A-2000342 AA 0.004715058 AA 3387.764 1027.536
SNP_A-4268173 AA 0.003301703 AA 1745.539 245.1303

Total number of rows: 909622

Table truncated, full table size 44157 Kbytes.




Supplementary file Size Download File type/resource
GSM463217_071218CHM023.CEL.gz 31.9 Mb (ftp)(http) CEL
GSM463217_071218CHM023.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463217_071218CHM023.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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