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Sample GSM463212 Query DataSets for GSM463212
Status Public on May 17, 2010
Title CHM018
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 0.01975096 AA 2361.692 704.1135
SNP_A-1967418 BB 0.01140461 BB 358.6095 709.217
SNP_A-1969580 BB 0.001486438 BB 1354.25 4543.174
SNP_A-4263484 BB 0.008642633 BB 407.7483 1808.937
SNP_A-1978185 AA 0.00318524 AA 1552.586 358.6095
SNP_A-4264431 AA 0.00272892 AA 1997.689 379.9138
SNP_A-1980898 BB 0.001082938 BB 265.3955 863.4141
SNP_A-1983139 BB 0.0058272 BB 388.4317 1789.399
SNP_A-4265735 BB 0.01159541 BB 346.4692 1135.267
SNP_A-1995832 BB 0.008193523 BB 392.084 1302.169
SNP_A-1995893 BB 0.004792371 BB 421.8398 2178.853
SNP_A-1997689 BB 0.01095798 BB 797.4716 3459.788
SNP_A-1997709 AA 0.004579436 AA 1427.74 256.2183
SNP_A-1997896 AA 0.005815227 AA 1602.605 587.9313
SNP_A-1997922 BB 0.005868219 BB 592.6064 1158.744
SNP_A-2000230 BB 0.00232234 BB 1125.237 3961.033
SNP_A-2000332 BB 0.00555605 BB 1201.7 3314.033
SNP_A-2000337 AA 0.003802808 AA 1981.621 261.4869
SNP_A-2000342 AA 0.002033157 AA 3616.882 892.468
SNP_A-4268173 AA 0.001766343 AA 1904.012 306.2703

Total number of rows: 909622

Table truncated, full table size 44106 Kbytes.

Supplementary file Size Download File type/resource
GSM463212_071218CHM018.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM463212_071218CHM018.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463212_071218CHM018.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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