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Sample GSM463284 Query DataSets for GSM463284
Status Public on May 17, 2010
Title CHM102
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 0.007632645 AA 2836.774 747.6146
SNP_A-1967418 AA 0.002386915 AA 887.0028 298.1377
SNP_A-1969580 BB 0.006274084 BB 1677.926 5046.589
SNP_A-4263484 AA 0.006435738 AA 2250.104 454.4255
SNP_A-1978185 AA 0.01329097 AA 1332.586 413.3642
SNP_A-4264431 BB 0.0009885785 BB 496.1871 1555.274
SNP_A-1980898 BB 0.007118112 BB 257.5529 703.5433
SNP_A-1983139 AA 0.003575746 AA 2350.902 675.7653
SNP_A-4265735 BB 0.001432674 BB 496.16 1504.467
SNP_A-1995832 BB 0.001439634 BB 525.16 1571.651
SNP_A-1995893 BB 0.004576162 BB 478.1301 2787.192
SNP_A-1997689 BB 0.00146268 BB 868.0784 4157.024
SNP_A-1997709 AA 0.004878907 AA 1410.416 257.7611
SNP_A-1997896 AA 0.006901409 AA 1534.201 600.7372
SNP_A-1997922 BB 0.003017772 BB 591.7274 1277.388
SNP_A-2000230 AA 0.006136289 AA 2802.479 1225.575
SNP_A-2000332 BB 0.001359569 BB 1180.846 3580.632
SNP_A-2000337 AA 0.002468531 AA 2133.998 349.2547
SNP_A-2000342 AA 0.006751391 AA 3323.51 1066.419
SNP_A-4268173 AA 0.005334052 AA 2024.578 298.1377

Total number of rows: 909622

Table truncated, full table size 44122 Kbytes.

Supplementary file Size Download File type/resource
GSM463284_071219CHM102.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM463284_071219CHM102.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463284_071219CHM102.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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