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Sample GSM377513 Query DataSets for GSM377513
Status Public on Mar 01, 2010
Title human embryonic stem cell line H7 s6 p230
Sample type genomic
 
Source name human embryonic stem cell line H7 s6 p230
Organism Homo sapiens
Characteristics cell type: human embryonic stem cell
cell line: H7 s6 p230
gender: female
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 0.003604 BB 800.637512 3831.084473
SNP_A-1967418 AB 0.013926 AB 641.637695 457.677155
SNP_A-1969580 BB 0.007771 BB 914.140564 4251.141602
SNP_A-4263484 AB 0.006020 AB 1500.166382 899.537903
SNP_A-1978185 AA 0.001413 AA 1278.095093 406.444458
SNP_A-4264431 AA 0.004077 AA 2053.189697 413.944397
SNP_A-1980898 BB 0.004224 BB 315.291168 981.727356
SNP_A-1983139 AA 0.021009 AA 2917.758301 1002.466980
SNP_A-4265735 AA 0.001720 AA 2110.149170 473.738525
SNP_A-1995832 AB 0.003308 AB 1902.245361 1574.163818
SNP_A-1995893 AB 0.014023 AB 1856.913818 2399.860596
SNP_A-1997689 BB 0.000575 BB 607.306213 3225.182373
SNP_A-1997709 AA 0.004080 AA 1459.516968 249.980728
SNP_A-1997896 AB 0.003211 AB 997.677612 1649.910767
SNP_A-1997922 AA 0.014521 AA 811.191833 370.733521
SNP_A-2000230 AB 0.003509 AB 1184.265015 1686.523804
SNP_A-2000332 AB 0.002535 AB 2520.543213 2429.015381
SNP_A-2000337 AA 0.005373 AA 1221.021240 316.075012
SNP_A-2000342 AA 0.004071 AA 3353.224121 894.694519
SNP_A-4268173 AB 0.002112 AB 872.423157 776.431580

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.




Supplementary file Size Download File type/resource
GSM377513.CEL.gz 28.1 Mb (ftp)(http) CEL
GSM377513.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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