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Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [bulk]

ABSTRACT: Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [bulk]

PROVIDER: PRJNA416036 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6223670.fastq.gz	Fastqsanger.gz
	SRR6223680.fastq.gz	Fastqsanger.gz
	SRR6223671.fastq.gz	Fastqsanger.gz
	SRR6223681.fastq.gz	Fastqsanger.gz
	SRR6223672.fastq.gz	Fastqsanger.gz

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Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids

Project description:Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids

| PRJNA415967 | ENA

Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [individual]

Project description:Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [individual]

| PRJNA415971 | ENA

Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [E6.5 to E9.5]

Project description:Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [E6.5 to E9.5]

| PRJNA454332 | ENA

Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [individual]

Project description:Gastruloids, small aggregates of murine Embryonic Stem (ES) cells stimulated to undergo gastrulation-like symmetry breaking events in vitro (van den Brink, S. C. et al. 2014, Simunovic, M. & Brivanlou, A. H 2017). Analysis of the transcriptional profiles from pools of gastruloids collected at different time-points after aggregation (AA) revealed that gastruloids are capable of organizing an axially integrated post-occipital pattern of neural, mesodermal and endodermal derivatives that mimics that of the embryo in terms of gene expression. To test the homogeneity and reproducibility of the transcriptional programs uncovered by our bulked RNAseq experiments, we performed RNAseq analysis of individual gastruloids collected at different time-points AA (10 biological replicates per time-point). Our results indicates that the transcriptional profiles of gastruloid were highly reproducible at each time points and that each gastruloid implement the full diversity of transcriptional programs detected in our bulked RNAseq experiments.

2018-06-01 | GSE106226 | GEO

Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [bulk]

Project description:Gastruloids are small aggregates of murine Embryonic Stem (ES) cells stimulated to undergo gastrulation-like symmetry breaking events in vitro (van den Brink, S. C. et al. 2014, Simunovic, M. & Brivanlou, A. H 2017). We analyzed the transcriptomic profiles of gastruloids at different time-points after aggregation (AA), showing that they are capable of organizing a post-occipital pattern of neural, mesodermal and endodermal derivatives that mimics that of the embryo in terms of gene expression.

2018-06-01 | GSE106225 | GEO

Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids [E6.5 to E9.5]

Project description:Gastruloids are small aggregates of murine Embryonic Stem (ES) cells stimulated to undergo gastrulation-like symmetry breaking events in vitro (van den Brink, S. C. et al. 2014, Simunovic, M. & Brivanlou, A. H 2017). We analyzed the transcriptomic profiles of gastruloids at different time-points after aggregation (AA) and compared them with those of mouse embryo at different stages, raging from e6 to e9.5. We show that gastruloids are capable of organizing a post-occipital pattern of neural, mesodermal and endodermal derivatives that mimics that of the embryo in terms of gene expression.

2018-06-01 | GSE113885 | GEO

Notch coordinates self-organization of germ layers and axial polarity in cnidarian gastruloids

Project description:Notch coordinates self-organization of germ layers and axial polarity in cnidarian gastruloids

| PRJNA1327231 | ENA

Multi-axial self-organisation properties of mouse embryonic stem cells into gastruloids

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-06-01 | GSE106227 | GEO

Notch coordinates self-organization of germ layers and axial polarity in cnidarian gastruloids

Project description:Dissociation and reaggregation experiments in several animal systems have revealed the stunning capacity of self-organization. Reaggregated early gastrula cells (here called gastruloids) of the sea anemone Nematostella vectensis are able to regenerate with only little delay whole organisms that are virtually indistinguishable from normal developing polyps. However, the molecular control underlying the restoration of body axis and germ layers remains largely unknown. To address this, we established a standardized protocol, which reproducibly generates gastruloids developing into polys with a single body axis. Here, we show that committed mesodermal and endodermal cells are sorted out to the surface of the aggregate, where mesodermal cells form clusters of about 30 cells. At a critical time point, one mesodermal cluster immigrates, along with peripherally attached endodermal cells. Thereby, the inner germ layer and the oral-aboral axis is established in one and the same process. Functional studies demonstrated that this polarization of the endodermal cells requires a feedback loop of Notch and Wnt signaling. The dissociation of the early embryo disrupts Notch signaling in the endodermal cells, which leads to transient adoption of an endomesodermal profile, marked by the expression of the mesodermal cadherin1 until the boundaries between the germ layer identities are re-established. Our results highlight distinct morphogenetic behaviors of mesodermal and endodermal cells and the hitherto unknown role of Notch signaling in germ layer boundary formation in self-organizing gastruloids. Conservation of Notch-mediated boundary formation between endoderm and mesoderm mirrors bilaterian mechanisms, demonstrating how adoption of ancestral regulatory networks governing morphogenesis likely enabled the diversification of metazoan body plans.

2025-09-15 | GSE307733 | GEO

Cadherins modulate the self-organizing potential of gastruloids (re-analysis)

Project description:Gastruloids have recently emerged as an efficient four-dimensional model for studying some aspects of post-implantation embryonic patterning. Their ability to undergo gastrulation-like processes leading to the self-organization into highly reproducible biological objects, has opened new avenues to investigate early embryonic patterning. Here, we sought to uncover the molecular and cellular mechanism underlying this remarkable property. We report that self-organization competence is associated with a cell-specific coordination of a Cadherin switch. We find that N-Cadherin hinders gastruloids morphogenetic competence, for its inactivation leads to the formation of trunk-like structures without relying on the otherwise requested extra-cellular matrix analogues such as Matrigel. In contrast, the repression of E-Cadherin by Snai1 is critical for self-organization: Snai1 establishes a cell-specific repressive pace by triggering the repression of a pluripotency-associated transcription program and its chromatin landscape, thus allowing a proper transition from E- to N-Cadherin to occur. Altogether, this work establishes a molecular mechanism that integrates the exit from pluripotency and the pace of cell differentiation, leading to the observed self-organizing potential of gastruloids.

2024-07-18 | GSE247510 | GEO

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