NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE15096 Query DataSets for GSE15096
Status Public on Mar 01, 2010
Title Affymetrix SNP 6.0 array data for human embryonic stem cell lines
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Pluripotent human embryonic stem cells are studied for potential applications in regenerative cell replacement therapies because of their untransformed nature and unique capacity to self-renew and differentiate. However it is known that adaptation of hESCs occurs on prolonged culture and may be associated with the acquisition of chromosome abnormalities.
We report a high resolution DNA SNP 6.0 array analysis showing copy number variation in 17 different hESC lines maintained in different laboratories. Several of the changes were culture induced and changed the expression levels of affected genes. Loss of heterozygosity (LOH) of chromosome 16q was detected in one line, in addition to several smaller LOH regions. Importantly, hESCs were found to contain several CNVs less than 3 Mb in size which is below the detection limit of conventional karyotyping.
 
Overall design Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 29 hESC samples of various passages and laboratory origin. 40 reference HapMap samples from Affymetrix were hybridized at the same time to built a reference genome used in the analysis.
 
Contributor(s) Närvä EM, Autio R, Rahkonen N, Kong L, Harrison N, Kitsberg D, Borghese L, Itskovitz-Eldor J, Rasool O, Dvorak P, Hovatta O, Otonkoski T, Tuuri T, Cui W, Brüstle O, Baker D, Maltby E, Moore HD, Benvenisty N, Andrews PW, Yli-Harja O, Lahesmaa R
Citation(s) 20351689
Submission date Mar 04, 2009
Last update date Nov 27, 2018
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
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (69)
GSM377509 human embryonic stem cell line H7s14 p30
GSM377510 human embryonic stem cell line H7s14 p38
GSM377511 human embryonic stem cell line H7 s6 p128
This SubSeries is part of SuperSeries:
GSE15097 High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines
Relations
BioProject PRJNA123109

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE15096_RAW.tar 2.7 Gb (http)(custom) TAR (of CEL, CHP)
Processed data provided as supplementary file
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap