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Sample GSM463247 Query DataSets for GSM463247
Status Public on May 17, 2010
Title CHM059
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 BB 0.002456184 BB 1014.069 3412.593
SNP_A-1967418 AB 0.05664582 AB 646.253 361.3046
SNP_A-1969580 BB 0.001630256 BB 1181.29 4375.809
SNP_A-4263484 AA 0.002129035 AA 2533.063 482.9058
SNP_A-1978185 AA 0.001450408 AA 1850.862 442.8679
SNP_A-4264431 AA 0.001573224 AA 1808.575 356.4179
SNP_A-1980898 BB 0.00652462 BB 247.7289 715.4717
SNP_A-1983139 AA 0.005327488 AA 2270.024 666.5139
SNP_A-4265735 BB 0.001150328 BB 503.8343 1567.254
SNP_A-1995832 BB 0.001850497 BB 610.7076 1868.487
SNP_A-1995893 BB 0.001145178 BB 437.3361 2534.653
SNP_A-1997689 BB 0.001847085 BB 954.7001 4506.085
SNP_A-1997709 AA 0.003923616 AA 1532.788 279.6426
SNP_A-1997896 AA 0.003374688 AA 1684.131 544.4739
SNP_A-1997922 BB 0.002396572 BB 559.436 1203.25
SNP_A-2000230 AA 0.006959538 AA 3629.968 1711.626
SNP_A-2000332 AA 0.003572551 AA 3197.986 762.857
SNP_A-2000337 AA 0.006423513 AA 1545.815 336.6352
SNP_A-2000342 AA 0.004118378 AA 3375.052 994.7397
SNP_A-4268173 AA 0.003332024 AA 1991.383 340.7664

Total number of rows: 909622

Table truncated, full table size 44107 Kbytes.

Supplementary file Size Download File type/resource
GSM463247_071217CHM059.CEL.gz 31.7 Mb (ftp)(http) CEL
GSM463247_071217CHM059.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463247_071217CHM059.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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