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Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_concentration]

ABSTRACT: Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_concentration]

PROVIDER: PRJNA1216293 | ENA |

REPOSITORIES: ENA

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Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids

Project description:Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids

| PRJNA1216289 | ENA

Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_time]

Project description:Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_time]

| PRJNA1216285 | ENA

Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_time]

Project description:Understanding the interplay between cell fate specification and morphogenetic changes remains a central challenge in developmental biology. Gastruloids, self-organizing pseudo-embryos that mimic post-implantation mammalian development, provide a powerful platform to address this question. Here, we show that physical parameters, particularly system size, critically influence the timing and outcomes of morphogenetic processes. Larger gastruloids exhibit delayed symmetry breaking, increased multipolarity, and prolonged axial elongation, with morphogenesis driven by system size. Despite these variations, transcriptional programs and cell fate composition remain remarkably stable across a broad size range. Notably, extreme sizes show distinct transcriptional modules and clear shifts in gene expression patterns. Intriguingly, size perturbation experiments rescued the morphogenetic and pattern phenotypes observed in extreme sizes, demonstrating the remarkable adaptability of gastruloids to their effective system size. These findings establish gastruloids as versatile models for studying spatiotemporal dynamics in mammalian embryogenesis and reveal how physical constraints decouple transcriptional from morphogenetic programs.

2025-09-08 | GSE288155 | GEO

Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids [RNAseq_concentration]

2025-09-08 | GSE288157 | GEO

Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids

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

2025-09-08 | GSE288158 | GEO

Hypoxia induces a transcriptional primitive streak signature in ES cells and enhances lineage patterning in gastruloids

Project description:The cellular microenvironment shapes stem cell identity and differentiation capacity. Mammalian early embryos are exposed to hypoxia in vivo and benefit from hypoxic culture in vitro. Yet, how different components of the hypoxia response impact stem cell transcriptional networks and lineage choices remains unclear. Here we investigated the effect of acute and prolonged hypoxia on stem cell states and differentiation efficiencies of embryonic and extraembryonic cells. We show that prolonged hypoxia enhances differentiation of embryonic stem (ES) cells towards the mesendoderm lineage by transcriptionally priming cells with a primitive streak signature including Wnt3 and T expression. Exposure to hypoxia in ES culture or during formation of gastrulation-mimicking organoids (gastruloids) moderates T expression and enhances structural complexity. Hypoxic gastruloids generated without exogenous Wnt induction can spontaneously elongate and self-organize. Direct gene regulation by Hif1a, combined with DNA demethylation and metabolic rewiring modulate the transcriptional response and phenotypic outcome. Our findings highlight the influence of the microenvironment on stem cell function and provide a rationale supportive of applying physiological conditions in synthetic embryo models.

2022-09-05 | PXD026641 | Pride

Bulk RNAseq of mouse gastruloids developed with homemade N2B27 and commercial NDiff227

Project description:Procedure: three independent experiments were done to generate three 96-well plates of E14-Tg2A gastruloids made with either homemade or commercial N2B27. 48 gastruloids per sample were used for RNA extraction using the Qiagen RNeasy Micro Kit. Library preparation and sequencing were done by the CRG Genomics Facility (Spain). Sequencing was done in a NextSeq 2000 and generated around 30M paired-end reads per sample.

2025-04-01 | E-MTAB-14893 | biostudies-arrayexpress

Single Cell RNA-seq time course of mouse gastruloids at 0h (mESCs), 24h, 48h and 72h post-aggregation

Project description:Single cell transcriptomic study (using 10x Genomics v3 kits) of gastruloids, aggregates of mESCs, at different developmental timepoints (24h, 48h and 72h post-aggregation). mESCs, corresponding to the 0h timepoint, were also sequenced. The aim of this study was to delineate the cell state transition dynamics underlying anteroposterior symmetry breaking and germ layer formation in gastruloids. Gastruloids used in this study were generated from Bra::GFP reporter mESCs (Fehling et al., 2003).

2023-12-04 | E-MTAB-12749 | biostudies-arrayexpress

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

Project description:Gastruloids are three-dimensional aggregates of embryonic stem cells (ESCs) that display key features of mammalian post-implantation development, including germ layer specification and axial organization. Gastruloids have mostly been characterized with microscopy-based approaches, limiting the number of genes that can be explored. It is therefore unclear to what extent gene expression in gastruloids reflects in vivo embryonic expression. Using both single-cell RNA-seq (scRNA-seq) and spatial transcriptomics we systematically compared cell types and spatial expression patterns between mouse gastruloids and mouse embryos.

2019-12-05 | GSE123187 | GEO

YAP1 Drives Lineage Specification and Patterning in hESC-derived Gastruloids

Project description:The gastrulation process is controlled by the interplay between morphogenetic signals from BMP, WNT and NODAL pathways. Increasing evidences support an emerging role of the Hippo-YAP signaling in the cell-fate decisions that guide lineage specification in mouse and human Embryonic Stem Cells (hESCs). However, the contribution of YAP to the process of gastrulation in hESCs remains unknown. Here, we show that YAP1 regulates the specification, size and patterning of the three-germ layers. Using hESC-derived 2D-micropatterned gastruloids and directed differentiation approaches we show that YAP maintains a semi-active NODAL signaling during gastrulation essential to regulate the exit of pluripotency. In absence of YAP1, a hyperactive NODAL signaling retains SMAD2.3 in the nuclei, impeding the exit of pluripotency and the acquisition of the ectodermal gene program. Accordingly, the inhibition of NODAL signaling is sufficient to rescue the gastrulation-defective phenotype of the YAP1 KO hESCs. Our work revealed that Hippo-YAP1 signaling is an important component of the developmental network that coordinate hESC pluripotency and gastrulation.

2022-01-14 | GSE168377 | GEO

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