GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM463198 Query DataSets for GSM463198
Status Public on May 17, 2010
Title CHM002
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 0.01194313 AA 4247.576 1109.199
SNP_A-1967418 BB 0.01478114 BB 408.3743 863.8138
SNP_A-1969580 BB 0.006816811 BB 1283.663 5201.883
SNP_A-4263484 AA 0.008874758 AA 3129.754 455.9754
SNP_A-1978185 AA 0.01130148 AA 2121.59 599.0131
SNP_A-4264431 BB 0.002557566 BB 432.4054 1543.388
SNP_A-1980898 BB 0.01018678 BB 328.1017 988.5747
SNP_A-1983139 AA 0.003776115 AA 2435.58 761.7432
SNP_A-4265735 BB 0.006124905 BB 375.8025 1556.783
SNP_A-1995832 AA 0.003225825 AA 2023.024 476.7813
SNP_A-1995893 AA 0.00781289 AA 2208.738 1298.448
SNP_A-1997689 BB 0.00538514 BB 892.6992 4949.405
SNP_A-1997709 AA 0.01009488 AA 2567.558 278.6979
SNP_A-1997896 AA 0.00112188 AA 1466.378 469.4877
SNP_A-1997922 AA 0.03109782 AA 1675.18 396.1399
SNP_A-2000230 AA 0.0007831956 AA 3365.249 1432.823
SNP_A-2000332 BB 0.0009514461 BB 1253.056 3823.148
SNP_A-2000337 AA 0.002568937 AA 2055.327 373.4133
SNP_A-2000342 AA 0.0008162331 AA 3729.342 975.6077
SNP_A-4268173 AA 0.002821974 AA 1964.16 344.0895

Total number of rows: 909622

Table truncated, full table size 44109 Kbytes.

Supplementary file Size Download File type/resource
GSM463198_071215CHM002.CEL.gz 30.7 Mb (ftp)(http) CEL
GSM463198_071215CHM002.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463198_071215CHM002.birdseed-v2.chp.txt.gz 15.0 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