Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Laminin111-based defined culture promoting self-renewing human pluripotent stem cells exhibiting properties of early post-implantation epiblast cells [LN_hPSC_SC]

ABSTRACT: In our study we sought to develop cultures highly enriched for self-renewing human pluripotent stem cells (hPSCs) with an early post-implantation phenotype, capturing the formative pluripotency phase in vitro. Our results demonstrate that hPSCs cultured on LN111 in defined conditions (LN-hPSCs) generate cultures highly enriched for genetically stable, self-renewing hPSCs exhibiting properties similar to the early-post implantation epiblast, including competence to give rise to the germ cell lineage. To analyze the global transcriptome of LN-hPSCs in comparison with conventional/primed and naive hPSCs, we performed RNA-seq of the three hPSC lines cultured under LN, primed, and naïve conditions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE206712 | GEO | 2022/11/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Laminin111-based defined culture promoting self-renewing human pluripotent stem cells exhibiting properties of early post-implantation epiblast cells [LN_hPSC_RRBS]

Project description:In our study we sought to develop cultures highly enriched for self-renewing human pluripotent stem cells (hPSCs) with an early post-implantation phenotype, capturing the formative pluripotency phase in vitro. Our results demonstrate that hPSCs cultured on LN111 in defined conditions (LN-hPSCs) generate cultures highly enriched for genetically stable, self-renewing hPSCs exhibiting properties similar to the early-post implantation epiblast, including competence to give rise to the germ cell lineage. To analyze the global transcriptome of LN-hPSCs in comparison with conventional/primed and naive hPSCs, we performed RNA-seq of the three hPSC lines cultured under LN, primed, and naïve conditions.

2022-11-13 | GSE206711 | GEO

Laminin111-based defined culture promoting self-renewing human pluripotent stem cells exhibiting properties of early post-implantation epiblast cells [Bulk_RNA_Seq]

2022-11-13 | GSE206708 | GEO

Derivation of trophoblast stem cells from naïve human pluripotent stem cells [RNA-seq]

Project description:Naïve human pluripotent stem cells (hPSCs) provide a unique experimental platform of cell fate decisions during pre-implantation development, but their lineage potential remains incompletely characterized. As naïve hPSCs share transcriptional and epigenomic signatures with trophoblast cells, it has been proposed that the naïve state may have enhanced predisposition for differentiation along this extraembryonic lineage. Here we examined the trophoblast potential of isogenic naïve and primed hPSCs. We found that naïve hPSCs can directly give rise to human trophoblast stem cells (hTSCs) and undergo further differentiation into both extravillous and syncytiotrophoblast. In contrast, primed hPSCs do not support hTSC derivation, but give rise to non-self-renewing cytotrophoblasts in response to BMP4. Global transcriptome and chromatin accessibility analyses indicate that hTSCs derived from naïve hPSCs acquire features of pre-implantation trophectoderm. The derivation of hTSCs from naïve hPSCs will enable elucidation of early mechanisms that govern normal human trophoblast development and associated pathologies.

2020-02-13 | GSE138688 | GEO

Derivation of trophoblast stem cells from naïve human pluripotent stem cells [ATAC-seq]

2020-02-13 | GSE138761 | GEO

Stirred suspension bioreactors maintain naïve pluripotency of human pluripotent stem cells (hPSCs)

Project description:Although cell therapies require large numbers of quality-controlled hPSCs, existing technologies are limited in their ability to efficiently grow and scale stem cells. We report here that cell-state conversion from primed-to-naïve pluripotency enhances the biomanufacturing of hPSCs. Naïve hPSCs exhibit superior growth kinetics and aggregate formation characteristics in stirred suspension bioreactors compared to their primed counterparts. Moreover, we demonstrate the role of the bioreactor mechanical environment in the maintenance of naïve pluripotency, through transcriptomic enrichment of mechano-sensing signaling for cells in the bioreactor along with a decrease in expression of lineage-specific and primed pluripotency hallmarks. Bioreactor-cultured, naïve hPSCs express epigenetic regulatory transcripts associated with naïve pluripotency, and display hallmarks of X-chromosome reactivation. They exhibit robust production of naïve pluripotency metabolites and display reduced expression of primed pluripotency cell surface markers. We also show that these cells retain the ability to undergo targeted differentiation into beating cardiomyocytes, hepatocytes, and neural rosettes. They additionally display faster kinetics of teratoma formation compared to their primed counterparts. Naïve bioreactor hPSCs also retain structurally stable chromosomes. Our research corroborates that converting hPSCs to the naïve state enhances hPSC manufacturing and indicates a potentially important role for the bioreactor’s mechanical environment in maintaining naïve pluripotency.

2020-05-08 | ST001377 | MetabolomicsWorkbench

Gene expression profile at single cell level for induction of human primordial germ cell-like cells (hPGCLCs) in a biomimetic culture

Project description:Transcriptome at the single-cell level of a biomimetic culture of primed human pluripotent stem cells (hPSCs) was profiled at Day 3 and Day 8. The biomimetic culture, which mimics the peri-implantation human epiblast development, provides an easily implementable culture protocol for deriving human primordial germ cell-like cells (hPGCLCs) from primed hPSCs .

2022-06-10 | GSE205611 | GEO

RNA-sequencing analysis of naive and primed hPSCs in static and stirred suspension conditions

Project description:We have pioneered human pluripotent stem cell (hPSC) manufacturing in stirred suspension bioreactors. Cell therapies require large numbers of quality-controlled hPSCs yet technologies are limited in their ability to efficiently grow and scale clinically-viable hPSCs. We report here that naive hPSCs exhibit superior growth in suspension bioreactors compared to their primed counterpart. Naive hPSCs exhibited a shorter lag phase, and grew into more uniform, homogenous aggregates. Compared to static culture, gene expression analyses revealed that the bioreactor environment promoted the upregulation of naïve- and downregulation of primed-associated transcripts in both primed and naive hPSCs. Bioreactor-cultured naive hPSCs similarly showed more hypomethylated DNA and less primed hPSC-associated surface protein marker compared to statically-cultured naive hPSCs. Gene expression, epigenetic, and cell surface protein marker analyses all suggest that the bioreactor environment promotes the transition from primed-to-naive pluripotent state. Our research shows that reprogramming conventional hPSCs to the naive pluripotent state enhances hPSC manufacturing.

2020-08-31 | GSE125041 | GEO

Reversion to naïve human pluripotency creates a new methylation landscape devoid of blastocyst or germline memory

Project description:Human embryonic stem cells (hESCs) typically exhibit "primed" pluripotency, analogous to stem cells derived from the mouse post-implantation epiblast. This has led to a search for growth conditions that support self-renewal of hESCs akin to hypomethylated naïve epiblast cells in human pre-implantation embryos. We have discovered that reverting primed hESCs to a hypomethylated naïve state or deriving a new hESC line under naïve conditions results in the establishment of Stage Specific Embryonic Antigen 4 (SSEA4) negative hESC lines with a transcriptional program resembling the human pre-implantation epiblast. In contrast, we discovered that the methylome of naïve hESCs in vitro is distinct from the human epiblast in vivo with loss of DNA methylation at primary imprints and a lost "memory" of the methylation state of the human oocyte. This failure to recover the naïve epiblast methylation landscape appears to be a consistent feature of self-renewing hypomethylated naïve hESCs in vitro.

2016-02-04 | GSE76970 | GEO

Stabilization of virgin naïve hESCs in two distinct substates along the continuum of pluripotency [miRNA-seq]

Project description:A detailed understanding of the developmental substates of human pluripotent stem cells (hPSCs) is needed to optimize their use in cell therapy and models of early development. Genetic instability and risk of tumorigenicity of primed hPSCs are well documented, but a systematic isogenic comparison between primed and naive substates has not been previously performed. We derived four hESC lines in naïve conditions and generated isogenic pairs of naïve and primed cultures. Through phenotypic, mRNA, miRNA, and DNA methylation profiling, we identified changes that arose during the naïve-primed transition and over extended culture. Although early naïve hESC cultures showed greater proliferation and clonogenic potential compared to primed cultures, they drifted toward a more primed-like substate over time, including accumulation of genetic abnormalities. Overall, we show that transcriptomic and epigenomic profiling can be used to place naïve/primed cultures along a developmental continuum, and may inform their utility for clinical and research applications.

2022-11-03 | GSE208301 | GEO

Stabilization of virgin naïve hESCs in two distinct substates along the continuum of pluripotency [RNA-seq]

2022-11-03 | GSE208300 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data