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Gene expression difference in cells expressing high and low FoxA2-Venus protein levels from mouse neural tube organoids.

ABSTRACT: Gene expression difference in cells expressing high and low FoxA2-Venus protein levels from mouse neural tube organoids.

PROVIDER: PRJNA913173 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22777644.fastq.gz	Fastqsanger.gz
	SRR22777645.fastq.gz	Fastqsanger.gz
	SRR22777646.fastq.gz	Fastqsanger.gz
	SRR22777647.fastq.gz	Fastqsanger.gz
	SRR22777648.fastq.gz	Fastqsanger.gz

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Gene expression difference in cells expressing high and low FoxA2-Venus protein levels from mouse neural tube organoids.

Project description:We describe the transcriptomic differences in FoxA2-Venus high and low cell populations in neural tube organoids.

2024-04-24 | GSE221187 | GEO

Comparison of Hob6-Venus positive and negative Flk-1+ cells (Venus reporter)

Project description:ES derived Flk-1+ cells were separated by sorting into Hoxb6 positive and negative populations by Venus reporter. Gene expression was compared between these two groups. Duplicate analysis of Hoxb6-Venus positive and negative Flk-1+ cells.

2013-04-16 | E-GEOD-45191 | biostudies-arrayexpress

RNAseq analysis of FACs sorted E-cadherin+, Kit+ and K5-venus+ cells from E15 K5-venus mouse submandibular salivary glands

Project description:We used embryonic day 15 submandibular salivary glands from K5-Venus mice, which were produced using the bovine-K5 promoter driving Venus expression, N=3 separate experiments

2017-01-01 | GSE89896 | GEO

Comparison of Hob6-Venus positive and negative Flk-1+ cells (Venus reporter)

Project description:ES derived Flk-1+ cells were separated by sorting into Hoxb6 positive and negative populations by Venus reporter. Gene expression was compared between these two groups.

2013-04-16 | GSE45191 | GEO

Gene expression profile of Huh7 cells upon knock-down of FOXA2 or FOXA2-DS-S

Project description:We used siRNAs to knock-down the gene FOXA2 and the positionally-conserved ncRNA (pcRNA) FOXA2-DS-S is Huh7. We have shown that FOXA2 regulates its own expression by binding its promoter, but it can also affect the expression of the associated pcRNA FOXA2-DS-S. At the same time, we have shown that FOXA2-DS-S is necessary for the expression of the FOXA2 gene. These data suggest that the pcRNA acts locally, in cis, to regulate the expression of FOXA2. With this microarray experiment with aimed to explore further the genome-wide transcriptional effects of FOXA2-DS-S or FOXA2 knock-down.

2018-01-09 | E-MTAB-4517 | biostudies-arrayexpress

Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition

Project description:Organoids can undergo pattern formation by spontaneously forming spatially-localised signaling centers called organisers. Understanding how molecular pathways participate in this regulative process is a central challenge in biology. Here, we investigated self-organisation of a SHH-expressing floorplate in clonal neural tube organoids (NTOs). In NTOs, a pulse of retinoic acid (RA) applied at Day 2 triggers self-organisation of a FOXA2+ floorplate by Day 6. FOXA2 expression was initially spatially scattered before resolving into multiple clusters. These FOXA2+ clusters underwent competition and physical sorting, resulting in a stable “winning” floorplate. We identified BMP signalling as a key governor of long-range cluster competition.

2024-04-23 | GSE236543 | GEO

Foxa2 overexpression is sufficient to establish the p3 neural progenitor chromatin landscape

Project description:In many developing tissues the spatial and temporal pattern of gene expression is organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. The morphogen Sonic hedgehog (Shh) acts in a graded manner to direct neural progenitor specification in the neural tube. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. A common set of CREs are used to control gene activity in the majority of ventral neural progenitors. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for Foxa2-mediated cell specification across tissues.

2022-06-06 | GSE204664 | GEO

Chromatin immunopreciptiation of liver from wild type and Foxa2 knock out mice to identify Foxa2 binding sites

Project description:In order to identify the subset of genes directly regulated by Foxa2 in the liver, we performed genome-wide location analysis. Chromatin immunoprecipitation (ChIP) samples from livers of wild type and Foxa2 liver-conditional null mice (Foxa2loxP/loxPAlfp.Cre) were hybridized to a mouse enhancer/promoter microarray with more than 36,000 elements (BCBCPromChip 5). This analysis identified 574 enhancer and promoter regions, corresponding to 484 unique genes, as occupied by Foxa2 in the adult liver.

2008-07-14 | E-MEXP-1675 | biostudies-arrayexpress

Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition

Project description:The neural tube (NT) has been a hallmark example of embryonic induction and patterning whereby the notochord induces an organiser, the floorplate, that secretes Sonic Hedgehog (SHH) to pattern the surrounding field of neural progenitors. On the other hand, NT organoids (NTOs) formed from embryonic stem cells (ESCs) undergo spontaneous floorplate formation and patterning in the absence of their normal embryonic inducers. Understanding how stem cells undergo regulative organiser formation is a central challenge in biology. Here, we investigated the self-organisation of a SHH-expressing floorplate organiser using clonal mouse NTOs. Expression of FOXA2, a floorplate transcription factor, was initially spatially scattered before resolving into multiple clusters. These FOXA2+ clusters underwent competition and physical sorting, resulting in a stable “winning” floorplate. We identified BMP signalling as a key governor of long-range cluster competition. FOXA2+ clusters expressed BMP4 ligand suppressing FOXA2 in receiving cells, while simultaneously expressing the BMP-inhibitor NOGGIN to secure FOXA2+ cluster survival. Genetic mutation of Noggin perturbed the floorplate not only in NTOs but also in vivo at the mid-hindbrain region of the mouse NT. These results demonstrate how the floorplate can form autonomously without its well-known inducer, the notochord, suggesting redundant mechanisms ensuring robustness. Defining molecular pathways that govern organiser self-organisation is critical in harnessing the developmental plasticity of stem cells toward directed tissue engineering.

2024-04-23 | GSE260579 | GEO

Foxa2 identifies a novel ventricular-specific cardiac progenitor population during gastrulation.

Project description:The recent identification of novel progenitor populations that contribute to the developing heart in a distinct temporal and spatial manner has fundamentally improved our understanding of cardiac development. However, little remains known about cardiac specification events prior to the establishment of the heart tube, or the mechanisms that direct atrial versus ventricular specification. We have identified a novel progenitor population that gives rise specifically to cardiovascular cells of the ventricles but not the atria, and to the epicardium of the differentiated heart. We determined that this cell population is first specified during gastrulation, when it transiently expresses Foxa2, a gene not previously implicated in cardiac development. Using chimeric mosaic analysis we further demonstrate that Foxa2 is cell-autonomously required for the development of ventricular cells. Finally, we reveal the existence of an analogous Foxa2+ cardiac mesoderm population during in vitro differentiation from embryonic stem cells and illustrate that these cells express genes relevant for heart development. Our data thus describe the first progenitor population identified as early as gastrulation that displays ventricular-specific differentiation potential. Together, these findings provide important new insights into the developmental origin of ventricular and atrial myocytes, and will lead to the establishment of new strategies for generating these cell types from pluripotent stem cells.

2017-02-08 | GSE78964 | GEO

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