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Sample GSM463283 Query DataSets for GSM463283
Status Public on May 17, 2010
Title CHM101
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 0.003265162 AA 3812.449 815.4092
SNP_A-1967418 BB 0.01555341 BB 322.3495 1095.355
SNP_A-1969580 BB 0.004187027 BB 1475.134 4546.985
SNP_A-4263484 BB 0.003730223 BB 657.2505 1982.81
SNP_A-1978185 BB 0.003336076 BB 979.2689 3193.296
SNP_A-4264431 BB 0.001421833 BB 485.3152 1428.67
SNP_A-1980898 BB 0.004477268 BB 208.3429 857.2488
SNP_A-1983139 AA 0.009994891 AA 2168.87 752.6293
SNP_A-4265735 BB 0.008108901 BB 611.8633 1766.1
SNP_A-1995832 AA 0.02746887 AA 2975.323 427.097
SNP_A-1995893 AA 0.00602771 AA 2554.061 1323.709
SNP_A-1997689 BB 0.004552425 BB 969.5352 4860.581
SNP_A-1997709 AA 0.01698751 AA 2517.867 230.1198
SNP_A-1997896 AA 0.01426269 AA 1787.561 655.6541
SNP_A-1997922 AA 0.003496224 AA 1333.431 333.0596
SNP_A-2000230 AA 0.002144455 AA 3556.135 1337.447
SNP_A-2000332 AA 0.0038796 AA 3588.137 956.4119
SNP_A-2000337 AA 0.008319429 AA 1479.018 402.6499
SNP_A-2000342 AA 0.0003988864 AA 3818.942 975.0142
SNP_A-4268173 AA 0.001558198 AA 1738.944 272.8411

Total number of rows: 909622

Table truncated, full table size 44113 Kbytes.

Supplementary file Size Download File type/resource
GSM463283_071219CHM101.CEL.gz 31.1 Mb (ftp)(http) CEL
GSM463283_071219CHM101.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463283_071219CHM101.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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