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Sample GSM463223 Query DataSets for GSM463223
Status Public on May 17, 2010
Title CHM031
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 0.002201087 AA 3682.517 785.107
SNP_A-1967418 BB 0.003763669 BB 260.2867 905.7559
SNP_A-1969580 BB 0.003030278 BB 1536.132 4952.138
SNP_A-4263484 BB 0.002415835 BB 587.7097 1868.538
SNP_A-1978185 BB 0.009341801 BB 718.4646 3204.691
SNP_A-4264431 BB 0.006611571 BB 548.1249 1309.06
SNP_A-1980898 BB 0.005840246 BB 236.0733 736.7559
SNP_A-1983139 BB 0.01075812 BB 291.9439 1859.984
SNP_A-4265735 BB 0.005766529 BB 536.0384 1430.969
SNP_A-1995832 BB 0.005454451 BB 709.8018 1670.295
SNP_A-1995893 BB 0.003903974 BB 422.9298 2220.225
SNP_A-1997689 BB 0.007824309 BB 918.7472 3697.272
SNP_A-1997709 AA 0.009539253 AA 1439.649 179.6645
SNP_A-1997896 AA 0.01270703 AA 1128.517 591.7991
SNP_A-1997922 BB 0.008844278 BB 361.9196 1030.244
SNP_A-2000230 AA 0.0172869 AA 2616.155 1544.529
SNP_A-2000332 AA 0.008460012 AA 2924.715 686.1607
SNP_A-2000337 AA 0.004053057 AA 1707.254 396.0892
SNP_A-2000342 AA 0.01081953 AA 2934.801 984.5394
SNP_A-4268173 AA 0.004091478 AA 1646.004 237.123

Total number of rows: 909622

Table truncated, full table size 43995 Kbytes.

Supplementary file Size Download File type/resource
GSM463223_071218CHM031.CEL.gz 31.4 Mb (ftp)(http) CEL
GSM463223_071218CHM031.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463223_071218CHM031.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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