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Sample GSM463240 Query DataSets for GSM463240
Status Public on May 17, 2010
Title CHM051
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 0.001567003 AA 3622.302 798.2521
SNP_A-1967418 BB 0.005868973 BB 240.8193 741.1683
SNP_A-1969580 BB 0.004133011 BB 1559.591 5216.823
SNP_A-4263484 BB 0.003981427 BB 456.468 2034.702
SNP_A-1978185 AA 0.006416233 AA 1429.852 339.0655
SNP_A-4264431 AA 0.004961437 AA 2110.311 384.3074
SNP_A-1980898 BB 0.004800399 BB 236.6936 758.2092
SNP_A-1983139 AA 0.003399035 AA 2797.712 760.9373
SNP_A-4265735 BB 0.005578197 BB 445.5237 1711.409
SNP_A-1995832 BB 0.006022328 BB 664.7388 2110.221
SNP_A-1995893 BB 0.0009226881 BB 487.3013 2455.664
SNP_A-1997689 BB 0.001771232 BB 943.7682 4298.596
SNP_A-1997709 AA 0.003518024 AA 1573.435 232.9792
SNP_A-1997896 AA 0.01540515 AA 1913.791 645.8525
SNP_A-1997922 BB 0.002831758 BB 446.1095 1194.454
SNP_A-2000230 AA 0.005541265 AA 2862.144 1179.735
SNP_A-2000332 AA 0.00885534 AA 3683.426 829.3091
SNP_A-2000337 AA 0.01049907 AA 1570.929 261.4789
SNP_A-2000342 AA 0.003455997 AA 3387.448 937.3832
SNP_A-4268173 AA 0.02950425 AA 2461.341 447.6067

Total number of rows: 909622

Table truncated, full table size 44076 Kbytes.




Supplementary file Size Download File type/resource
GSM463240_071218CHM051.CEL.gz 31.5 Mb (ftp)(http) CEL
GSM463240_071218CHM051.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463240_071218CHM051.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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