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Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG]

ABSTRACT: We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used CUT&TAG to map H3K27ac- and H3K4me1-bound genomic regions and identify OTX2-bound enhancers during directed differentiation of EpiSCs to Primitive Streak (PS) intermediates and DE

ORGANISM(S): Mus musculus

PROVIDER: GSE294521 | GEO | 2025/07/21

REPOSITORIES: GEO

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Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm.

Project description:We discovered a role for the transcription factor OTX2 in formation of mouse definitive endoderm (DE). We used RNAseq to measure changes in gene expression and identify OTX2-regulated genes during directed differentiation of EpiSCs to Primitive Streak (PS) intermediates and DE

2025-07-21 | GSE293151 | GEO

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [scRNA_PS_Meso]

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 Primitive Streak (PS) and Paraxial Mesoderm (PM) using scRNA-seq. We used dTAG13 to deplete OTX2 at PS.

2025-07-21 | GSE293158 | GEO

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [PS_CUTnRUN]

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

2025-07-21 | GSE294520 | GEO

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

2024-06-26 | GSE254590 | GEO

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

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

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

Transcriptional remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm [CUTnTAG]

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

| PRJNA1250439 | ENA

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

2015-06-03 | GSE69547 | GEO

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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