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Sample GSM463197 Query DataSets for GSM463197
Status Public on May 17, 2010
Title CHM001
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 0.007195893 AA 4142.965 991.4983
SNP_A-1967418 BB 0.01606518 BB 273.7758 1083.995
SNP_A-1969580 BB 0.007420268 BB 1719.048 5397.535
SNP_A-4263484 BB 0.002398663 BB 616.1859 2093.239
SNP_A-1978185 AA 0.002372426 AA 1878.738 408.4299
SNP_A-4264431 AA 0.00914431 AA 2104.984 248.482
SNP_A-1980898 BB 0.006586248 BB 311.7585 962.7864
SNP_A-1983139 AA 0.00384239 AA 2821.114 765.1288
SNP_A-4265735 AA 0.002588096 AA 1251.943 453.65
SNP_A-1995832 BB 0.001509302 BB 554.9984 1819.175
SNP_A-1995893 BB 0.00288242 BB 485.5065 2712.791
SNP_A-1997689 BB 0.0009837503 BB 899.6049 4508.099
SNP_A-1997709 AA 0.0030069 AA 1785.814 310.6792
SNP_A-1997896 AA 0.005399468 AA 1882.058 427.7889
SNP_A-1997922 BB 0.003440791 BB 578.8943 1206.884
SNP_A-2000230 AA 0.00354972 AA 3315.303 1174.72
SNP_A-2000332 AA 0.01282763 AA 2817.431 631.2806
SNP_A-2000337 AA 0.004925315 AA 2306.526 292.9464
SNP_A-2000342 AA 0.002696799 AA 3918.514 862.9614
SNP_A-4268173 AA 0.007345264 AA 2121.534 336.9446

Total number of rows: 909622

Table truncated, full table size 44107 Kbytes.

Supplementary file Size Download File type/resource
GSM463197_071215CHM001.CEL.gz 31.8 Mb (ftp)(http) CEL
GSM463197_071215CHM001.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463197_071215CHM001.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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