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

ABSTRACT: 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

ORGANISM(S): Mus musculus

PROVIDER: GSE254428 | GEO | 2024/06/26

REPOSITORIES: GEO

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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: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

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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]

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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]

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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]

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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

Otx2 controls regional patterning within the MGE and regional identity of the septum [ChIP-Seq]

Project description:The Otx2 homeobox transcription factor is essential for gastrulation and early neural development. We generated Otx2 conditional knockout (cKO) mice to investigate its roles in telencephalon development after E9.0. We conducted transcriptional profiling and in situ hybridization to identify genes de-regulated in Otx2 cKO ventral forebrain. In parallel, we used ChIP-seq to identify enhancer elements, OTX2 binding motif, and which de-regulated genes are likely direct targets of Otx2 transcriptional regulation. We found that Otx2 was essential in septum specification; regulation of Fgf signaling in the rostral telencephalon; and medial ganglionic eminence (MGE) patterning, neurogenesis, and oligodendrogenesis. Within the MGE, Otx2 was required for ventral but not dorsal identity; this is the first demonstration of a transcription factor that contributes to regional patterning within the MGE. Microdissected subpallium (septum, MGE, and LGE ) from wildtype E12.5 CD-1 embryos was used in three independentanti-OTX2 ChIP-seq experiments.

2015-06-10 | E-GEOD-69724 | biostudies-arrayexpress

Otx2 controls regional patterning within the MGE and regional identity of the septum [Agilent]

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Otx2 controls regional patterning within the MGE and regional identity of the septum [ChIP-Seq]

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Otx2 binding to Nanog promoter protects embryonal stem cells from corruption of naive pluripotency and is required at morula stage for inner-cell mass differentiation of the epiblast

Project description:We have investigated the functional relevance of the transcriptional network controlled by the Otx2 binding activity in ESCs, EpiSCs and in vivo. In particular, to study the Otx2 transcriptional network we first performed Otx2 chromatin immunoprecipitation sequencing (ChIP-seq) experiments in wt ESCs and day 4 (d4) ESC-derived EpiSCs and employed as negative control ESCs and EpiSCs lacking Otx2. Moreover, to investigate the functional relevance of the Otx2 binding activity in pluripotent stem cells, we mutagenized in ESCs the Otx2 binding site located upstream of the Nanog TSS. To characterize the identity of ESCs and EpiSCs both lacking this Otx2 binding site, we analyzed their transcriptome by RNA-Seq.

2016-06-09 | E-MTAB-3856 | biostudies-arrayexpress

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