GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM463230 Query DataSets for GSM463230
Status Public on May 17, 2010
Title CHM039
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 0.002189212 AA 3685.271 788.2916
SNP_A-1967418 BB 0.003216251 BB 336.9582 885.0065
SNP_A-1969580 BB 0.001618618 BB 1234.575 4372.213
SNP_A-4263484 BB 0.006215805 BB 690.6898 2117.445
SNP_A-1978185 AA 0.007980596 AA 1868.254 578.5665
SNP_A-4264431 AA 0.006587305 AA 1765.658 421.3345
SNP_A-1980898 BB 0.01229666 BB 173.4745 787.2837
SNP_A-1983139 AA 0.0006767799 AA 2634.406 710.5363
SNP_A-4265735 BB 0.0008929978 BB 451.1316 1472.333
SNP_A-1995832 AA 0.0008344313 AA 2167.377 468.0593
SNP_A-1995893 AA 0.003294373 AA 2118.635 1096.505
SNP_A-1997689 BB 0.003823411 BB 939.8711 4819.593
SNP_A-1997709 AA 0.002121864 AA 2163.025 312.6159
SNP_A-1997896 AA 0.0001678094 AA 1584.068 477.1113
SNP_A-1997922 AA 0.0005946378 AA 1164.116 285.07
SNP_A-2000230 BB 0.001038398 BB 1085.066 4099.437
SNP_A-2000332 BB 0.001682672 BB 1202.125 3552.843
SNP_A-2000337 AA 0.0007487996 AA 1878.792 336.9582
SNP_A-2000342 AA 0.002911126 AA 3698.958 850.6624
SNP_A-4268173 AA 0.006148332 AA 1549.323 311.0157

Total number of rows: 909622

Table truncated, full table size 44170 Kbytes.

Supplementary file Size Download File type/resource
GSM463230_071218CHM039.CEL.gz 31.5 Mb (ftp)(http) CEL
GSM463230_071218CHM039.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463230_071218CHM039.birdseed-v2.chp.txt.gz 15.1 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap