Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA251888 | ENA |
REPOSITORIES: ENA
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Project description:Human embryonic stem cells (hESC) show great promise for clinical and research applications, but genomic instability hampers the development of their full potential. Here we demonstrate that increased culture density causes medium acidification due to lactic acid accumulation. hESC are able to cope with this, but acquire increased DNA damage associated to DNA replication stress. Also, single-cell genomics analysis reveals a strong correlation of the occurrence of de novo CNVs and culture density after only five days of culture. However, by an improved control over the accumulation of metabolites through more frequent medium changes, we were able to counter the effect of culture density on DNA damage and CNVs. These data underline the importance of optimal culture conditions, even at short-term, in the light of bringing hESC to their full potential.
2016-02-02 | GSE58281 | GEO
Project description:By analyzing five human embryonic stem (hES) cell lines over long-term culture, we detected a recurrent genomic instability in the human genome. An amplification of 2.5–4.6 Mb at 20q11.21, encompassing about 23 genes in common, appeared in four cell lines of different origins. This amplification, which has been associated with oncogenic transformation, may provide a selective advantage to hES cells in culture
2008-11-19 | GSE13565 | GEO
Project description:By analyzing five human embryonic stem (hES) cell lines over long-term culture, we detected a recurrent genomic instability in the human genome. An amplification of 2.5â4.6 Mb at 20q11.21, encompassing about 23 genes in common, appeared in four cell lines of different origins. This amplification, which has been associated with oncogenic transformation, may provide a selective advantage to hES cells in culture Array-based comparative genomic hybridization, was performed on genomic DNA samples from different human embryonic stem cell lines, all cultured in our laboratory under the same conditions. VUB05-HD is an hES cell line carrying the Huntingtin mutant gene H1, H9, SA01, and VUB01 are various hES cell lines GSM341552 and GSM341553: SNP analysis GSM341589 to GSM341669: CGH analysis
2010-05-16 | E-GEOD-13565 | biostudies-arrayexpress
Project description:Genomic instability of human embryonic stem cells in mechanic and enzymatic passaging culture
| PRJNA208331 | ENA
Project description:Human induced hepatic lineage-oriented stem cells (hiHSCs) can be established as a new type of human induced pluripotent stem cells (hiPSCs) with only some modifications of their culture conditions in both generation and self-renewal. hiHSCs were generated and expanded at a very high density under non-typical coculture with feeder cells in a chemically defined hiPSC medium . In detail, hiHSCs were generated from human non-hepatic cells by gene transfer with pantropic retrovirus vectors carrying the three transcription factor genes OCT3/4, SOX2, and KLF4. They were expanded at a very high density under non-typical coculture with mouse embryonic fibroblasts (MEF) in a chemically defined mTeSR1 medium on gelatin-coated dishes. Self-renewing hiHSCs expressed markers of both human embryonic stem cells (hESCs) and hepatocytes. The potential hepatic specification of hiHSCs was defined by their expression profiles of hepatic markers under a self-renewal culture.
2015-03-13 | GSE63844 | GEO
Project description:Fibroblast growth factors (FGFs) are essential for maintaining self-renewal in human embryonic stem cells and induced pluripotent stem cells. Recombinant basic FGF (bFGF or FGF2) is conventionally used to culture pluripotent stem cells; however, because of bFGF instability, repeated addition of fresh bFGF into the culture medium is required in order to maintain its concentration. In this study, we demonstrate that a heat-stable chimeric variant of FGF, FGFC, can be successfully used for maintaining human pluripotent stem cells. FGFC is a chimeric protein composed of human FGF1 and FGF2 domains that exhibits higher thermal stability and protease resistance than do both FGF1 and FGF2. Both human embryonic stem cells and induced pluripotent stem cells were maintained in ordinary culture medium containing FGFC instead of FGF2. Comparison of cells grown in FGFC with those grown in conventional FGF2 media, showed no significant differences in terms of the expression of pluripotency markers, global gene expression, karyotype, or differentiation potential into the three germ lineages. We therefore propose FGFC, as an effective alternative to FGF2, for maintenance of human pluripotent stem cells.
2017-02-09 | GSE55428 | GEO
Project description:Human embryonic stem cells in E8 and AKIT culture medium
| PRJNA358199 | ENA
Project description:X-inactivation is a paradigm of epigenetic transcriptional regulation. Human embryonic stem cells (hESCs) that harbor an inactivated X-chromosome often undergo erosion of X-inactivation upon prolonged culture. Here, we investigate the sources of X-inactivation instability by deriving new primed pluripotent hESC lines. We find that the composition of culture media dramatically influenced the expression of XIST lncRNA, a key regulator of X-inactivation. hESCs cultured in a defined medium stably maintained XIST RNA coating, whereas hESCs cultured in the widely-used mTeSR1 medium lost XIST RNA expression. We pinpointed lithium chloride in mTeSR1 as a cause of XIST RNA loss. The addition of LiCl or inhibitors of glycogen synthase kinase 3 (GSK-3) proteins, which are inhibited by lithium, to the defined hESC culture medium impeded XIST expression. Together, these data may reconcile the observed variations in X-inactivation in hESCs and inform the culture of pluripotent stem cells for disease modeling and regenerative medicine.
2022-03-11 | GSE157809 | GEO
Project description:We use a chemically defined medium to systemically examine cellular activities and the impact of medium components in high-density culture. We show that medium acidosis is the main factor that alters cell cycle, gene expression and cellular metabolism at high cell density. The low medium pH leads to inhibition of glucose consumption, cell cycle arrest, and subsequent cell death. At high cell density, the suppression of medium acidosis with sodium bicarbonate (NaHCO3) significantly increases culture capacity for stem cell survival, derivation, maintenance and differentiation.
2018-04-12 | GSE113016 | GEO
Project description:Analysis of undifferentiated KhES-1 human embryonic stem cells in growth factors-dependent (E8) and -independent (AKIT) culture medium. Results provide insight into genes differentially expressed in pluripotent states maintained by AKIT and E8 culture medium.
2017-07-01 | GSE92628 | GEO