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Sample GSM463222 Query DataSets for GSM463222
Status Public on May 17, 2010
Title CHM030
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 0.003689146 AA 3653.092 711.3019
SNP_A-1967418 BB 0.0001947976 BB 297.6572 841.8936
SNP_A-1969580 BB 0.003838905 BB 1314.109 5058.447
SNP_A-4263484 AA 0.002977798 AA 2411.94 443.3297
SNP_A-1978185 AA 0.004834297 AA 1484.046 344.9681
SNP_A-4264431 BB 0.0004878621 BB 486.1634 1529.099
SNP_A-1980898 BB 0.001637307 BB 262.6343 956.6881
SNP_A-1983139 AA 0.003514833 AA 2626.31 578.5269
SNP_A-4265735 BB 0.0250595 BB 487.2359 1066.813
SNP_A-1995832 AA 0.01144818 AA 1786.721 492.2184
SNP_A-1995893 AA 0.005015559 AA 2024.04 1001.21
SNP_A-1997689 BB 0.002898955 BB 776.9727 4567.427
SNP_A-1997709 AA 0.009852288 AA 2413.623 386.5858
SNP_A-1997896 AA 0.000613108 AA 1558.645 492.8524
SNP_A-1997922 AA 0.0006615205 AA 1206.407 281.5352
SNP_A-2000230 AA 0.003782502 AA 3008.093 1196.777
SNP_A-2000332 AA 0.004300367 AA 3053.064 766.1418
SNP_A-2000337 AA 0.004694893 AA 2067.594 248.1523
SNP_A-2000342 AA 0.00467421 AA 3368.607 854.2664
SNP_A-4268173 AA 0.001724293 AA 1911 332.2688

Total number of rows: 909622

Table truncated, full table size 44110 Kbytes.

Supplementary file Size Download File type/resource
GSM463222_071218CHM030.CEL.gz 31.1 Mb (ftp)(http) CEL
GSM463222_071218CHM030.CN5.CNCHP.txt.gz 20.3 Mb (ftp)(http) TXT
GSM463222_071218CHM030.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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