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Sample GSM377519 Query DataSets for GSM377519
Status Public on Mar 01, 2010
Title human embryonic stem cell line CCTL-10 p33
Sample type genomic
 
Source name human embryonic stem cell line CCTL-10 p33
Organism Homo sapiens
Characteristics cell type: human embryonic stem cell
cell line: CCTL-10 p33
gender: male
Treatment protocol None
Growth protocol Cell lines were grown according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol cell samples were harvested in each collaborative laboratorion, washed with PBS and sent as a frozen cell pellet to analysis laboratory. Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen)
Label TdT
Label protocol accordingly manufactures protocol
 
Hybridization protocol accordingly manufactures protocol
Scan protocol accordingly manufactures protocol
Description Hybridized in Finnish DNA Microarray Centre
Data processing For detecting copy number variation in the samples, we utilized Affymetrix Genotyping Console 3.0.1 and Birdseed v2-algorithm. Samples were normalized against 40 International HapMap samples for copy number variation (CNV), Loss of heterozygosity (LOH) and Single nucleotide polymorphism (SNP).
 
Submission date Mar 04, 2009
Last update date Jan 29, 2010
Contact name Elisa Maarit Närvä
E-mail(s) elisa.narva@btk.fi
Organization name University of Turku
Department Turku Centre for Biotechnology
Lab Riitta Lahesmaa
Street address Tykistönkatu 6
City Turku
ZIP/Postal code 20520
Country Finland
 
Platform ID GPL6801
Series (2)
GSE15096 Affymetrix SNP 6.0 array data for human embryonic stem cell lines
GSE15097 High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 BB 0.002859 BB 753.809814 4526.959473
SNP_A-1967418 BB 0.002672 BB 306.936554 745.152954
SNP_A-1969580 BB 0.010790 BB 1573.949707 5703.006836
SNP_A-4263484 AA 0.001390 AA 2321.598145 444.245758
SNP_A-1978185 AA 0.006270 AA 1034.849731 355.653137
SNP_A-4264431 AB 0.001425 AB 1128.777832 929.877747
SNP_A-1980898 BB 0.088906 BB 489.696503 857.294678
SNP_A-1983139 AA 0.009774 AA 3633.086426 972.534668
SNP_A-4265735 BB 0.001211 BB 570.749878 2097.605713
SNP_A-1995832 AB 0.000783 AB 1753.355835 1501.274780
SNP_A-1995893 AB 0.013976 AB 2078.591553 2148.200195
SNP_A-1997689 BB 0.005476 BB 551.258301 3428.165039
SNP_A-1997709 AA 0.001786 AA 1710.973755 292.202148
SNP_A-1997896 AB 0.010756 AB 1265.861816 1774.803833
SNP_A-1997922 AA 0.002179 AA 790.821594 248.149521
SNP_A-2000230 AA 0.005908 AA 2379.045166 912.532227
SNP_A-2000332 AA 0.022977 AA 4319.091309 703.503601
SNP_A-2000337 AA 0.002516 AA 1324.188965 327.879272
SNP_A-2000342 AA 0.009392 AA 3141.805176 563.155884
SNP_A-4268173 AA 0.008244 AA 1855.968384 312.405273

Total number of rows: 909622

Table truncated, full table size 46150 Kbytes.




Supplementary file Size Download File type/resource
GSM377519.CEL.gz 27.7 Mb (ftp)(http) CEL
GSM377519.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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