Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Emergence and patterning dynamics of mouse definitive endoderm

ABSTRACT: Emergence and patterning dynamics of mouse definitive endoderm

PROVIDER: PRJNA782003 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16989504_1.fastq.gz	Fastqsanger.gz
	SRR16989504_2.fastq.gz	Fastqsanger.gz
	SRR16989505_1.fastq.gz	Fastqsanger.gz
	SRR16989505_2.fastq.gz	Fastqsanger.gz
	SRR16989506_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Emergence and patterning dynamics of mouse definitive endoderm

Project description:The segregation of definitive endoderm (DE) from bi-potent mesendoderm progenitors leads to the formation of two distinct germ layers. Dissecting DE commitment and onset has been challenging as it occurs within a narrow spatio-temporal window in the embryo. Here we employ a novel dual Bra/Sox17 reporter cell line to study DE onset dynamics. We find Sox17 expression initiates in a few isolated cells in vivo within a temporally restricted window. Using 2D and 3D in vitro models, we show that DE cells emerge from mesendoderm progenitors at a temporally regular, but spatially stochastic pattern, which is subsequently arranged by self-sorting of Sox17+ cells. A subpopulation of Bra-high cells commits to a Sox17+ fate independent of external Wnt signal. Self-sorting coincides with up-regulation of E-cadherin but is not necessary for DE differentiation or proliferation. Our in vivo and in vitro results highlight basic rules governing DE onset and patterning through the commonalities and differences between these systems.

2021-12-13 | GSE189224 | GEO

Emergence and patterning dynamics of mouse-definitive endoderm.

Project description:The segregation of definitive endoderm (DE) from bipotent mesendoderm progenitors leads to the formation of two distinct germ layers. Dissecting DE commitment and onset has been challenging as it occurs within a narrow spatiotemporal window in the embryo. Here, we employ a dual Bra/Sox17 reporter cell line to study DE onset dynamics. We find Sox17 expression initiates in vivo in isolated cells within a temporally restricted window. In 2D and 3D in vitro models, DE cells emerge from mesendoderm progenitors at a temporally regular, but spatially stochastic pattern, which is subsequently arranged by self-sorting of Sox17 + cells. A subpopulation of Bra-high cells commits to a Sox17+ fate independent of external Wnt signal. Self-sorting coincides with upregulation of E-cadherin but is not necessary for DE differentiation or proliferation. Our in vivo and in vitro results highlight basic rules governing DE onset and patterning through the commonalities and differences between these systems.

| S-EPMC8693470 | biostudies-literature

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [ATAC-seq]

Project description:We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used ATAC-seq to identify open chromatin regions in OTX2-depleted definitive endoderm cells and identify sites with changed accessibility during DE differentiation

2024-06-26 | GSE254431 | GEO

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Expression data set]

Project description:The definitive endoderm germ layer is the provenance of multiple internal organs, including the lungs, liver, pancreas and intestines. Molecular events driving initial endoderm germ layer specification and subsequent anterior-posterior patterning of endoderm into distinct organ primordia remain largely cryptic. Through microarray analyses, we captured genome-wide transcriptional dynamics driving successive stages of endoderm development with the intent of identifying novel regulatory genes or diagnostic markers that respectively drive or mark endoderm committment. HES3 human embryonic stem cells (hESCs) were differentiated into highly homogeneous endodermal progenitor populations, and microarray analyses were conducted of six different populations at different tiers of the endodermal lineage hierarchy: undifferentiated hESCs, anterior primitive streak (day 1 of in vitro differentiation), definitive endoderm (day 3) and anterior foregut, posterior foregut or midgut/hindgut patterned endoderm populations (day 7). Additionally, we compared hESCs differentiated using two alternative endoderm induction protocols, serum-based or AFBLy-based differentiation (both day 3 of differentiation).

2013-11-07 | E-GEOD-52158 | biostudies-arrayexpress

Dynamic developmental signaling logic underlying lineage bifurcations during human endoderm induction and patterning from pluripotent stem cells [Expression data set]

2013-11-07 | GSE52158 | GEO

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUT&RUN]

Project description:We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&RUN to map OTX2-bound genomic regions and identify OTX2-regulated genes during directed differentiation of EpiSCs to DE

2024-06-26 | GSE254590 | GEO

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [ATAC-seq]

Project description:Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [ATAC-seq]

| PRJNA1070555 | ENA

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA-seq]

Project description:Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA-seq]

| PRJNA1070557 | ENA

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUT&RUN]

Project description:Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUT&RUN]

| PRJNA1071101 | ENA

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA-seq]

Project description:We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We determined the gene expression profiles during conversion of EpiSCs to DE using scRNA-seq. We used dTAG13 to deplete OTX2 at two timepoints of differentiation

2024-06-26 | GSE254428 | 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