Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Self-organization of human gastrulation upon in vitro attachment

ABSTRACT: Self-organization of human gastrulation upon in vitro attachment

PROVIDER: PRJNA937851 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR23595081_1.fastq.gz	Fastqsanger.gz
	SRR23595081_2.fastq.gz	Fastqsanger.gz
	SRR23595082_1.fastq.gz	Fastqsanger.gz
	SRR23595082_2.fastq.gz	Fastqsanger.gz
	SRR23595083_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Self-organization of human gastrulation upon in vitro attachment

Project description:Single cell RNA-seq profiling distinguished extra-embryonic populations and derivatives of three germ layers that match with the human gastrula at 16-19 days post fertilization.

2023-12-15 | GSE225893 | GEO

Recapitulating human peri-gastrulation development via self-organization of extended pluripotent stem cells

Project description:Recapitulating human peri-gastrulation development via self-organization of extended pluripotent stem cells

| PRJNA974153 | ENA

Recapitulating human peri-gastrulation development via self-organization of extended pluripotent stem cells

Project description:Stem cell models that replicate the gastrulation process in human embryos have been created, but they lack the essential extraembryonic cells needed for early embryonic development and patterning. Here, we introduce a robust and efficient method that prompts human extended pluripotent stem (EPS) cells to self-organize into embryo-like structures, called peri-gastruloids, which encompass both embryonic (epiblast) and extraembryonic (hypoblast) tissues. These peri-gastruloids simulate critical stages of human peri-gastrulation development, such as forming amniotic and yolk sac cavities, developing bilaminar and trilaminar embryonic discs, specifying primordial germ cells, initiating gastrulation, and early neurulation. Single-cell RNA sequencing unveiled transcriptomic characteristics of these human peri-gastruloids, which closely resemble the primary peri-gastrulation cell types found in human and non-human primates. Our results emphasize the remarkable self-organizing ability of EPS cells to generate advanced human embryo-like structures. This peri-gastruloid platform allows for further exploration beyond gastrulation and may potentially aid in the development of human fetal tissues for use in regenerative medicine.

2023-07-20 | GSE232861 | GEO

The emergence of human gastrulation upon in vitro attachment.

Project description:While studied extensively in model systems, human gastrulation remains obscure. The scarcity of fetal biological material as well as ethical considerations limit our understanding of this process. In vitro attachment of natural blastocysts shed light on aspects of the second week of human development in the absence of the morphological manifestation of gastrulation. Stem cell-derived blastocyst models, blastoids, provide the opportunity to reconstitute pre- to post-implantation development in vitro. Here we show that upon in vitro attachment, human blastoids self-organize a BRA+ population and undergo gastrulation. Single-cell RNA sequencing of these models replicates the transcriptomic signature of the human gastrula. Analysis of developmental timing reveals that in both blastoid models and natural human embryos, the onset of gastrulation as defined by molecular markers, can be traced to timescales equivalent to 12 days post fertilization. In all, natural human embryos and blastoid models self-organize primitive streak and mesoderm derivatives upon in vitro attachment.

| S-EPMC10828709 | biostudies-literature

Self-organization and symmetry breaking in intestinal organoid development

Project description:Self-organization and symmetry breaking in intestinal organoid development

| PRJNA476588 | ENA

In vitro culture of cynomolgus monkey embryos beyond gastrulation

Project description:Gastrulation is a milestone event of embryonic development, during which germ layers are specified and reassigned into the body plan. Due to the inaccessibility in vivo at this stage and the ethical limitations, gastrulation currently remains a mystery in primates. Here, we report the establishment of an in vitro system to culture cynomolgus monkey embryos after up to 20 days to develop beyond the initiation of gastrulation. The histology, immunostaining and single cell sequencing results showed that the in vitro cultured embryos largely recapitulated the key events of early post-implantation development, and initiated gastrulation in primates. Considering the high similarities between monkeys and humans, this system will provide a unique platform for the investigations of human early post-implantation development at physiological, pathological and environmental conditions.

2019-11-01 | GSE130114 | GEO

ran asters proteomics - Proteomic profiling of microtubule self-organization in M-phase

Project description:The main proteomics events driving the self-organization of MTs in M-phase cytoplasms are determined by obtaining the full proteomes of the RanGTP induced MT structures at different time points in Xenopus egg extracts.

2018-07-11 | PXD008306 | Pride

Spatial organization of endometrial gene expression at the onset of embryo attachment in pigs

Project description:Spatial organization of endometrial gene expression at the onset of embryo attachment in pigs

| PRJNA507985 | ENA

Self-organization of pluripotent stem cells into reproducible early embryonic developmental patterns through epigenome editing

Project description:During embryonic development, different embryonic cell types co-develop together where each cell type expresses specific fate-inducing transcription factors through activation of developmental non-coding regulatory elements and interactions with neighboring cells. Here, we hypothesized that cell-intrinsic activation of a minimum number of such endogenous regulatory elements is sufficient to self-organize PSCs into early embryonic models. Our results show that CRISPR activation of only two regulatory elements in the genome of pluripotent stem cells is sufficient to generate embryonic patterns that show spatial and molecular resemblance to that of pre-gastrulation mouse embryonic development. Quantitative single-cell live fluorescent imaging showed that emergence of the spatially-ordered embryonic pattern happens through intrinsic induction of cell fate that leads to an orchestrated collective cellular motion. Based on these results, we propose a straightforward approach to efficiently form 3D embryo models through intrinsic CRISPRa-based epigenome editing and independent of external signaling cues. CRISPRa-induced embryo models show highly consistent composition of major embryonic cell types that are spatially organized, with nearly 80% of the structures forming an embryonic cavity. Single cell transcriptomics confirmed the presence of main embryonic cell types in CRISRPa-induced embryo models with transcriptional similarity to pre-gastrulation mouse embryos and revealed novel signaling communication links between different embryonic cell types. Our findings demonstrate that self-organization of embryonic patterns through minimum intrinsic epigenome editing presents a promising approach for efficient production of stem cell-based embryo models with high consistency and will pave the way for future straightforward systematic CRISPR-based screening of embryo models

2024-03-01 | GSE256138 | GEO

The spatial self-organization within pluripotent stem cell colonies is continued in detaching aggregates (scRNA-Seq)

Project description:Colonies of induced pluripotent stem cells (iPSCs) reveal aspects of self-organization even under culture conditions that maintain pluripotent state. To investigate the dynamics of this process under spatial confinement we used either PDMS pillars or micro-contact printing of vitronectin. OCT4, E-cadherin, and NANOG were progressively upregulated within about 70 µm from the outer rim of iPSC colonies. Single-cell RNA-sequencing demonstrated that OCT4high subsets have pronounced up-regulation of the TGF-β pathway, particularly of NODAL and its inhibitor LEFTY, at the rim of the colonies. Furthermore, calcium-dependent cell-cell interaction seemed to be relevant for the self-organization. After 5 to 7 days, the iPSC colonies detached spontaneously from micro-contact printed substrates to form 3D aggregates. This new method allowed generation of embryoid bodies (EBs) of controlled size, without any enzymatic or mechanical treatment. Within the early 3D aggregates, the radial organization and differential gene expression continued in analogy to the changes observed during self-organization of flat iPSC colonies. Our results provide further insight into the gradual self-organization within iPSC colonies and at their transition into EBs.

2022-08-26 | GSE184603 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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