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Sample GSM463232 Query DataSets for GSM463232
Status Public on May 17, 2010
Title CHM041
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 0.0040099 AA 3772.468 921.0932
SNP_A-1967418 BB 0.004588291 BB 240.8999 787.0115
SNP_A-1969580 BB 0.004685743 BB 990.3231 4183.917
SNP_A-4263484 AA 0.006831108 AA 2930.139 356.0055
SNP_A-1978185 BB 0.01304462 BB 1049.161 4125.793
SNP_A-4264431 BB 0.004546583 BB 575.994 1439.84
SNP_A-1980898 BB 0.003210404 BB 286.5211 834.6998
SNP_A-1983139 AA 0.002866431 AA 2776.985 647.3971
SNP_A-4265735 BB 0.002056993 BB 447.3112 1408.639
SNP_A-1995832 BB 0.00621011 BB 399.9872 1563.988
SNP_A-1995893 BB 0.0005552765 BB 456.9092 2444.079
SNP_A-1997689 BB 0.001224101 BB 916.8615 4287.575
SNP_A-1997709 AA 0.005358234 AA 1378.287 256.4333
SNP_A-1997896 AA 0.003834093 AA 1355.616 418.9336
SNP_A-1997922 BB 0.006175883 BB 417.0224 1013.389
SNP_A-2000230 AA 0.001111369 AA 3356.861 1451.19
SNP_A-2000332 BB 0.004214894 BB 1350.81 3636.215
SNP_A-2000337 AA 0.0007501449 AA 1956.07 352.003
SNP_A-2000342 AA 0.00423858 AA 4178.688 868.0905
SNP_A-4268173 AA 0.001077261 AA 1755.448 282.1481

Total number of rows: 909622

Table truncated, full table size 44104 Kbytes.

Supplementary file Size Download File type/resource
GSM463232_071218CHM041.CEL.gz 30.8 Mb (ftp)(http) CEL
GSM463232_071218CHM041.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463232_071218CHM041.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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