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Sample GSM463238 Query DataSets for GSM463238
Status Public on May 17, 2010
Title CHM049
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 0.0006735332 AA 3470.317 770.6741
SNP_A-1967418 BB 0.01769918 BB 397.4785 736.0536
SNP_A-1969580 BB 0.001347491 BB 1236.657 4408.119
SNP_A-4263484 BB 0.005612762 BB 675.3643 1885.661
SNP_A-1978185 AA 0.004825831 AA 1575.146 449.7692
SNP_A-4264431 BB 0.004168678 BB 528.7115 1662.634
SNP_A-1980898 AA 0.01020336 AA 881.6403 215.2191
SNP_A-1983139 AA 0.006935608 AA 2612.137 859.3644
SNP_A-4265735 BB 0.001239832 BB 496.5307 1610.766
SNP_A-1995832 AA 0.002032982 AA 2346.672 432.524
SNP_A-1995893 AA 0.004987773 AA 2256.229 912.9546
SNP_A-1997689 BB 0.01144647 BB 979.2875 3604.94
SNP_A-1997709 AA 0.01121526 AA 2443.135 247.308
SNP_A-1997896 AA 0.00210409 AA 1663.086 429.9596
SNP_A-1997922 AA 0.005097126 AA 1064.222 202.0408
SNP_A-2000230 AA 0.003603991 AA 2971.878 1292.64
SNP_A-2000332 BB 0.001023282 BB 1252.693 3674.804
SNP_A-2000337 AA 0.003320418 AA 1742.481 388.0906
SNP_A-2000342 AA 0.006497511 AA 3168.035 879.0506
SNP_A-4268173 AA 0.009523508 AA 1931.047 431.5123

Total number of rows: 909622

Table truncated, full table size 44151 Kbytes.

Supplementary file Size Download File type/resource
GSM463238_071218CHM049.CEL.gz 31.4 Mb (ftp)(http) CEL
GSM463238_071218CHM049.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463238_071218CHM049.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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