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Sample GSM463229 Query DataSets for GSM463229
Status Public on May 17, 2010
Title CHM038
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 0.001632821 BB 890.2071 3461.755
SNP_A-1967418 BB 0.008415556 BB 279.9728 666.1195
SNP_A-1969580 BB 0.003177832 BB 1526.711 4832.561
SNP_A-4263484 AA 0.001754557 AA 2711.327 484.8531
SNP_A-1978185 BB 0.004762897 BB 943.8268 3078.256
SNP_A-4264431 BB 0.004551912 BB 402.9608 1406.234
SNP_A-1980898 BB 0.003002234 BB 282.813 828.917
SNP_A-1983139 BB 0.0009142077 BB 503.7089 1937.623
SNP_A-4265735 AA 0.003378491 AA 1178.17 379.1907
SNP_A-1995832 AA 0.001071445 AA 2148.327 465.1403
SNP_A-1995893 AA 0.007450209 AA 2276.442 863.5376
SNP_A-1997689 BB 0.009736087 BB 709.9974 3557.276
SNP_A-1997709 AA 0.00499813 AA 2396.881 297.4868
SNP_A-1997896 AA 0.01193194 AA 1005.822 448.3863
SNP_A-1997922 AA 0.01056959 AA 911.6599 211.2208
SNP_A-2000230 AA 0.001200835 AA 3198.982 1342.689
SNP_A-2000332 AA 0.001853793 AA 3139.473 883.5809
SNP_A-2000337 AA 0.01293291 AA 2592.861 302.182
SNP_A-2000342 AA 0.003028044 AA 3550.157 1022.793
SNP_A-4268173 AA 0.0003157752 AA 1823.704 306.911

Total number of rows: 909622

Table truncated, full table size 44110 Kbytes.

Supplementary file Size Download File type/resource
GSM463229_071218CHM038.CEL.gz 31.9 Mb (ftp)(http) CEL
GSM463229_071218CHM038.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463229_071218CHM038.birdseed-v2.chp.txt.gz 15.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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