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Sample GSM463274 Query DataSets for GSM463274
Status Public on May 17, 2010
Title CHM088
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 0.006728902 AA 3735.755 982.9599
SNP_A-1967418 BB 0.006014698 BB 362.4128 865.4169
SNP_A-1969580 BB 0.007394054 BB 1560.608 5509.366
SNP_A-4263484 BB 0.002907932 BB 641.1172 1995.649
SNP_A-1978185 AA 0.001679827 AA 1690.385 356.0606
SNP_A-4264431 AA 0.004966481 AA 2073.704 287.9904
SNP_A-1980898 BB 0.00307086 BB 280.3297 970.6403
SNP_A-1983139 BB 0.005892497 BB 648.2819 2169.681
SNP_A-4265735 BB 0.001959726 BB 488.2684 1647.777
SNP_A-1995832 BB 0.004190582 BB 695.8061 1746.949
SNP_A-1995893 BB 0.003222378 BB 474.8801 2290.693
SNP_A-1997689 BB 0.02064521 BB 904.1638 3180.115
SNP_A-1997709 AA 0.001144501 AA 1922.979 301.2278
SNP_A-1997896 AA 0.001393718 AA 1582.217 436.8479
SNP_A-1997922 BB 0.003728027 BB 573.0214 1181.725
SNP_A-2000230 AA 0.0029518 AA 3134.389 1199.665
SNP_A-2000332 AA 0.003913734 AA 3013.912 867.2023
SNP_A-2000337 AA 0.007441039 AA 1750.179 249.349
SNP_A-2000342 AA 0.002233098 AA 3518.171 929.8242
SNP_A-4268173 AA 0.002667119 AA 1769.305 255.4858

Total number of rows: 909622

Table truncated, full table size 44059 Kbytes.

Supplementary file Size Download File type/resource
GSM463274_071219CHM088.CEL.gz 30.9 Mb (ftp)(http) CEL
GSM463274_071219CHM088.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463274_071219CHM088.birdseed-v2.chp.txt.gz 15.0 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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