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Sample GSM463239 Query DataSets for GSM463239
Status Public on May 17, 2010
Title CHM050
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 0.0009045555 AA 3371.357 770.8907
SNP_A-1967418 BB 0.01842241 BB 247.7551 576.8683
SNP_A-1969580 BB 0.004472447 BB 1303.729 4202.441
SNP_A-4263484 AA 0.009443302 AA 2254.922 339.3961
SNP_A-1978185 AA 0.002787286 AA 1574.515 355.2666
SNP_A-4264431 AA 0.00387338 AA 1801.377 274.3612
SNP_A-1980898 BB 0.01319652 BB 243.2988 624.0172
SNP_A-1983139 AA 0.01002489 AA 2113.7 628.7833
SNP_A-4265735 BB 0.01962566 BB 401.0527 1023.335
SNP_A-1995832 BB 0.002331575 BB 490.8162 1694.358
SNP_A-1995893 BB 0.009235055 BB 385.2352 2011.402
SNP_A-1997689 BB 0.005577497 BB 903.0931 3819.376
SNP_A-1997709 AA 0.008129988 AA 1246.281 261.5892
SNP_A-1997896 AA 0.002388158 AA 1761.126 469.0107
SNP_A-1997922 NoCall 0.2712033 BB 400.1201 654.1319
SNP_A-2000230 AA 0.003841643 AA 2970.354 1344.346
SNP_A-2000332 AA 0.003326734 AA 3098.567 942.6225
SNP_A-2000337 AA 0.004985639 AA 2281.144 273.8296
SNP_A-2000342 AA 0.01492293 AA 3220.1 677.254
SNP_A-4268173 AA 0.001586562 AA 1706.016 305.2913

Total number of rows: 909622

Table truncated, full table size 43994 Kbytes.

Supplementary file Size Download File type/resource
GSM463239_071218CHM050.CEL.gz 32.2 Mb (ftp)(http) CEL
GSM463239_071218CHM050.CN5.CNCHP.txt.gz 20.4 Mb (ftp)(http) TXT
GSM463239_071218CHM050.birdseed-v2.chp.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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