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Sample GSM463221 Query DataSets for GSM463221
Status Public on May 17, 2010
Title CHM029
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
E-mail(s) hayashi.kenshi@gmail.com
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
ID_REF
VALUE Call
Confidence
Forced Call
Signal A
Signal B

Data table
ID_REF VALUE Confidence Forced Call Signal A Signal B
SNP_A-2131660 AA 0.008039426 AA 4240.708 971.0826
SNP_A-1967418 BB 0.006079953 BB 350.6494 948.4746
SNP_A-1969580 BB 0.005492942 BB 1033.822 3934.84
SNP_A-4263484 BB 0.0025637 BB 622.0634 1924.439
SNP_A-1978185 AA 0.01470137 AA 2245.937 481.0509
SNP_A-4264431 AA 0.003828135 AA 1706.591 365.921
SNP_A-1980898 BB 0.0003254859 BB 253.2014 881.954
SNP_A-1983139 BB 0.004004601 BB 428.6107 1815.414
SNP_A-4265735 BB 0.004507386 BB 468.4487 1716.279
SNP_A-1995832 BB 0.001542546 BB 619.5511 1668.18
SNP_A-1995893 BB 0.005602981 BB 413.8345 2142.623
SNP_A-1997689 BB 0.006517109 BB 1068.453 4829.666
SNP_A-1997709 AA 0.007567205 AA 1261.404 257.2402
SNP_A-1997896 AA 0.002096851 AA 1476.152 428.6107
SNP_A-1997922 BB 0.002794395 BB 533.2076 1142.221
SNP_A-2000230 AA 0.00574117 AA 3365.092 1646.992
SNP_A-2000332 AA 0.01039095 AA 3264.017 1160.413
SNP_A-2000337 AA 0.006671159 AA 1551.672 401.149
SNP_A-2000342 AA 0.003338271 AA 3528.005 1027.533
SNP_A-4268173 AA 0.008085093 AA 1467.267 280.9649

Total number of rows: 909622

Table truncated, full table size 44008 Kbytes.




Supplementary file Size Download File type/resource
GSM463221_071218CHM029.CEL.gz 30.4 Mb (ftp)(http) CEL
GSM463221_071218CHM029.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463221_071218CHM029.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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