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Sample GSM463228 Query DataSets for GSM463228
Status Public on May 17, 2010
Title CHM036
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 0.001359638 AA 3584.249 802.5473
SNP_A-1967418 AA 0.002973328 AA 879.2517 303.4038
SNP_A-1969580 BB 0.008478753 BB 1075.637 3737.229
SNP_A-4263484 AA 0.02547743 AA 2433.221 684.5427
SNP_A-1978185 AA 0.001714348 AA 1846.445 407.4288
SNP_A-4264431 AA 0.002125283 AA 1792.65 364.2845
SNP_A-1980898 AA 0.006251054 AA 1080.975 377.7779
SNP_A-1983139 AA 0.003378356 AA 2425.786 744.7372
SNP_A-4265735 BB 0.004846383 BB 573.7435 1682.697
SNP_A-1995832 AA 0.001423011 AA 2155.515 504.4906
SNP_A-1995893 AA 0.01055412 AA 1856.462 1023.905
SNP_A-1997689 BB 0.002373384 BB 754.6054 4268.266
SNP_A-1997709 AA 0.003621829 AA 1849.415 323.1387
SNP_A-1997896 AA 0.02598356 AA 1362.576 224.3623
SNP_A-1997922 AA 0.005051144 AA 1182.459 367.0339
SNP_A-2000230 AA 0.002154382 AA 3168.701 1242.008
SNP_A-2000332 AA 0.003682207 AA 3574.519 938.6107
SNP_A-2000337 AA 0.008312145 AA 1729.052 244.8008
SNP_A-2000342 AA 0.001829157 AA 3667.827 891.1461
SNP_A-4268173 AA 0.002634267 AA 1960.854 327.7406

Total number of rows: 909622

Table truncated, full table size 44050 Kbytes.

Supplementary file Size Download File type/resource
GSM463228_071218CHM036.CEL.gz 31.9 Mb (ftp)(http) CEL
GSM463228_071218CHM036.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463228_071218CHM036.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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