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Series GSE34982 Query DataSets for GSE34982
Status Public on Mar 29, 2015
Title Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions I
Organism Homo sapiens
Experiment type Expression profiling by array
Methylation profiling by genome tiling array
SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary The self-renewal and differentiation capacities of human pluripotent stem cells (hPSCs) make them good sources of cells for cell transplantation therapy, drug development, and studies of cellular differentiation and development. However, the large numbers of cells necessary for many of these applications require extensive expansion of hPSC cultures, a process that has been associated with applications require extensive expansion of hPSC cultures, a process that has been associated with genetic and epigenetic alterations. We have performed a systematic study over more than 100continuous passages to identify characteristics of culture conditions (including passage method, substrate, and media type) that influence the genetic and epigenetic stability and the phenotypic characteristics of hPSCs. The predominant effects we observed were increased genetic instability with enzymatic passage, higher cell proliferation with feeder-free substrate, and variations among cultures in global gene expression and DNA methylation with time in culture. We observed recurrent duplications in two genomic regions that have been noted in earlier studies to be hotspots for duplication in hPSCs, as well as a previously unreported recurrent deletion of the tumor suppressor gene TP53 in all but one of the long-term culture conditions; the exception was the condition using mechanical passaging on feeder layers. The deletion of TP53 is associated with decreased mRNA expression of TP53, as well as alterations in the expression of several other genes in the TP53 pathway, which taken together indicate a decrease in the function of the TP53 pathway. Our results highlight the need for careful assessment of effects of culture conditions on cells intended for clinical therapies.
 
Overall design Total RNA extracted at different passages from Human Embryonic Stem Cells in different culture conditions. Total DNA extracted at different passages from Human Embryonic Stem Cells in different culture conditions.
 
Contributor(s) Garitaonandia I, Boscolo FS, Wambua G, Schultheiz H, Waltz S, Wang Y, Tran H, Leonardo T, Nazor K, Slavin I, Lynch C, Li Y, Coleman R, Seldeen JR, Gallego-Romero I, Altun G, Parast M, Loring JF, Laurent LC
Citation(s) 25714340
Submission date Jan 10, 2012
Last update date Mar 22, 2019
Contact name Francesca Boscolo
E-mail(s) francesca.boscolo@gmail.com
Organization name UCSD
Department Reproductive Medicine
Lab Marianna Alperin
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92122
Country USA
 
Platforms (3)
GPL6884 Illumina HumanWG-6 v3.0 expression beadchip
GPL8882 Illumina HumanOmni1-Quad BeadChip
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (183)
GSM859712 hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepA
GSM859713 hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepB
GSM859714 hESCs cultured on mouse feeder layer and mechanically passaged P2 mRNA RepC
This SubSeries is part of SuperSeries:
GSE56851 Increased Risk of Genetic and Epigenetic Instability in Human Embryonic Stem Cells Associated with Specific Culture Conditions
Relations
BioProject PRJNA151099

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
GSE34982_Matrix_Processed_Genotyping.txt.gz 1.3 Gb (ftp)(http) TXT
GSE34982_Matrix_Signal_Intensities_Genotyping.txt.gz 989.0 Mb (ftp)(http) TXT
GSE34982_Matrix_Signal_Intensities_Methylation.txt.gz 87.0 Mb (ftp)(http) TXT
GSE34982_RAW.tar 189.4 Mb (http)(custom) TAR
GSE34982_non-normalized_all_probes.txt.gz 22.0 Mb (ftp)(http) TXT
Processed data included within Sample table
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