Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition

ABSTRACT: Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition

PROVIDER: PRJNA1070582 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR27764648.fastq.gz	Fastqsanger.gz
	SRR27764649.fastq.gz	Fastqsanger.gz
	SRR27764650.fastq.gz	Fastqsanger.gz
	SRR27764651.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Gene expression profile of neighboring cells of cells with unfit Wnt morphogen gradient during cell competition

Project description:Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength-dependent manner to pattern developing tissues. However, developing tissues also undergo dynamic morphogenesis, which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradient. Here we show that a cell competition-related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/β-catenin signalling gradient, which acts as a morphogen to establish embryonic anterior-posterior patterning, revealed that unfit cells with abnormal Wnt/β-catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/β-catenin gradient formation and consequent anterior-posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues, this system may support tissue robustness and disease prevention.

2024-11-15 | GSE254439 | GEO

Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition

2019-09-15 | GSE133526 | GEO

Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition

Project description:Gene expression profile of cells with unfit Wnt morphogen gradient during cell competition

| PRJNA551686 | ENA

Soh2020 - Spatio-temporal morphogen gradient and BMP signaling

Project description:This model couples BMP morphogen gradient formation with Smad signaling in zebrafish and reproduces Fig.3B of the referenced paper. mBMP4 diffuses and forms a morphogen gradient in the host tissue where differential signal transduction kinetics for pSmad2 versus pSmad5 lead to narrow (pSmad2) versus wide (pSmad5) signal activity ranges in response to the same morphogen gradient (mBMP4) as input. The model file is in MorpheusML format and can be opened in the free, open-source multicellular modeling software Morpheus (https://morpheus.gitlab.io) to simulate the time course (movie) of the spatio-temporal dynamics. Further optional plots of the radial solution profile and the time courses of mean concentrations over the domain are included and temporarily inactivated in the model file, in section Analysis.

2021-10-06 | MODEL2012070002 | BioModels

Patterning ganglionic eminences in developing human brain organoids using morphogen gradient inducing device

Project description:In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brainin vitro. Here, we developed a method by assembling polydimethylsiloxane (PDMS) devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termedMorphogen-gradientInducedBrainOrganoids (MIBOs). At 3.5 weeks, MIBOs replicated Dorsal-Ventral patterning observed in the Ganglionic Eminence (GE). Analysis of matured MIBOs through single-cell RNA sequencing revealed distinct Dorsal GE derived CALB2+ interneurons (INs), Medium Spiny Neurons (MSNs), and MGE derived cell types. Finally, we demonstrate long term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling.

2024-02-14 | GSE244281 | GEO

Patterning ganglionic eminences in developing human brain organoids using morphogen gradient inducing device

Project description:Patterning ganglionic eminences in developing human brain organoids using morphogen gradient inducing device

| PRJNA1022059 | ENA

A microfluidic platform for anterior-posterior human endoderm patterning via countervailing morphogen gradients in vitro

Project description:Understanding how morphogen gradients spatially pattern tissues is a fundamental question in developmental biology but can be difficult to directly address using conventional approaches. Here we expose hPSC-derived endoderm cells to countervailing gradients of anteriorizing and posteriorizing signals using a widely available microfluidic device. This approach yielded spatially patterned cultures comprising anterior foregut (precursor to the thyroid, esophagus, and lungs) and mid/hindgut (precursor to the intestines) cells, whose identities were confirmed using single-cell RNA-sequencing. By exposing stem cells to externally applied signaling gradients, this widely accessible microfluidic platform should accelerate the production of spatially patterned tissues, complementing internally self-organizing organoids. Applying artificial morphogen gradients in vitro may also illuminate signaling gradient interpretation mechanisms that are otherwise challenging to study in mammalian embryos in vivo.

2024-12-25 | GSE285075 | GEO

Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning in the zebrafish embryo.

Project description:Morphogen signalling forms an activity gradient and instructs cell identities in a signalling strength-dependent manner to pattern developing tissues. However, developing tissues also undergo dynamic morphogenesis, which may produce cells with unfit morphogen signalling and consequent noisy morphogen gradients. Here we show that a cell competition-related system corrects such noisy morphogen gradients. Zebrafish imaging analyses of the Wnt/β-catenin signalling gradient, which acts as a morphogen to establish embryonic anterior-posterior patterning, identify that unfit cells with abnormal Wnt/β-catenin activity spontaneously appear and produce noise in the gradient. Communication between unfit and neighbouring fit cells via cadherin proteins stimulates apoptosis of the unfit cells by activating Smad signalling and reactive oxygen species production. This unfit cell elimination is required for proper Wnt/β-catenin gradient formation and consequent anterior-posterior patterning. Because this gradient controls patterning not only in the embryo but also in adult tissues, this system may support tissue robustness and disease prevention.

| S-EPMC6797755 | biostudies-literature

Morphogen-signalling modifying factors in Panarthropoda

Project description:morphogen-signalling modifying factors in Panarthropoda

| PRJEB28122 | ENA

Generating human neural diversity with a multiplexed morphogen screen in organoids

Project description:Morphogens choreograph the generation of remarkable cellular diversity in the developing nervous system. Differen-tiation of stem cells toward particular neural cell fates in vitro often relies upon combinatorial modulation of these signaling pathways. However, the lack of a systematic approach to understand morphogen-directed differentiation has precluded the generation of many neural cell populations, and knowledge of the general principles of regional specification remain incomplete. Here, we developed an arrayed screen of 14 morphogen modulators in human neu-ral organoids cultured for over 70 days. Leveraging advances in multiplexed RNA sequencing technology and anno-tated single cell references of the human fetal brain we discovered that this screening approach generated consid-erable regional and cell type diversity across the neural axis. By deconvoluting morphogen-cell type relationships, we extracted design principles of brain region specification, including critical morphogen timing windows and combinatorics yielding an array of neurons with distinct neurotransmitter identities. Tuning GABAergic neural sub-type diversity unexpectedly led to the derivation of primate-specific interneurons. Taken together, this serves as a platform towards an in vitro morphogen atlas of human neural cell differentiation that will bring insights into hu-man development, evolution, and disease.

2023-05-30 | GSE233574 | 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