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Sample GSM463281 Query DataSets for GSM463281
Status Public on May 17, 2010
Title CHM099
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
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
Forced Call
Signal A
Signal B

Data table
ID_REF VALUE Confidence Forced Call Signal A Signal B
SNP_A-2131660 AA 0.009454449 AA 4161.54 818.257
SNP_A-1967418 BB 0.007447843 BB 295.7258 1008.524
SNP_A-1969580 BB 0.006403364 BB 953.2288 3905.64
SNP_A-4263484 BB 0.005294044 BB 505.2867 2232.375
SNP_A-1978185 AA 0.0440983 AA 2429.571 782.821
SNP_A-4264431 BB 0.003370098 BB 522.0635 1375.836
SNP_A-1980898 BB 0.006964577 BB 235.3341 716.2422
SNP_A-1983139 AA 0.0005732721 AA 2579.265 705.2764
SNP_A-4265735 BB 0.008576175 BB 518.5045 1860.03
SNP_A-1995832 BB 0.002042969 BB 644.1972 1753.48
SNP_A-1995893 BB 0.004310396 BB 433.1808 2718.917
SNP_A-1997689 BB 0.01763593 BB 1150.304 5378.682
SNP_A-1997709 AA 0.01561126 AA 1433.817 347.1047
SNP_A-1997896 AA 0.002611649 AA 1660.821 532.6069
SNP_A-1997922 BB 0.006989012 BB 618.6098 1495.176
SNP_A-2000230 AA 0.02564605 AA 3449.255 2007.392
SNP_A-2000332 BB 0.002948384 BB 1191.091 3454.552
SNP_A-2000337 AA 0.0107843 AA 1564.189 463.1016
SNP_A-2000342 AA 0.002995006 AA 3748.192 1060.118
SNP_A-4268173 AA 0.006756551 AA 1688.775 205.0202

Total number of rows: 909622

Table truncated, full table size 43982 Kbytes.

Supplementary file Size Download File type/resource
GSM463281_071219CHM099.CEL.gz 30.7 Mb (ftp)(http) CEL
GSM463281_071219CHM099.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463281_071219CHM099.birdseed-v2.chp.txt.gz 15.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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