Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation [scRNA-Seq]

ABSTRACT: In this study, we characterised transcriptomes of mESC in different conditions EPSCM and KOSR subsetting them for their single expression of SOX2 or the double expression of SOX2 and GATA6 in these conditions. 2iLIF (sorted only by DAPI negative cells) were used as control.

ORGANISM(S): Mus musculus

PROVIDER: GSE227888 | GEO | 2023/12/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation [CUT&RUN]

Project description:In early mammalian development, cleavage stage blastomeres and cells of the inner cell mass (ICM) of the blastocyst co-express embryonic and extra-embryonic transcriptional determinants. Using a double protein-based reporter we identify embryonic stem cells (ESC) that co-express the extra-embryonic factor GATA6 alongside the embryonic factor SOX2 in specific conditions. Based on single cell transcriptomics we find these population resemble unsegregated ICM, exhibiting enhanced differentiation potential for endoderm while maintaining epiblast competence and suggesting they represent an ideal model to determine how GATA6 and SOX2 influence each other's DNA binding. To relate this binding to future fate, we describe a complete enhancer set in both ESCs and naïve extraembryonic endoderm stem cells and ask whether SOX2 and GATA6 recognize these elements in ICM-like ESC sub-population. Both factors support cooperative recognition in these lineages, with GATA6 bound alongside SOX2 on a fraction of pluripotency enhancers and SOX2 alongside GATA6 more extensively on endoderm enhancers. Our findings suggest that cooperative binding between these antagonistic factors both supports self-renewal and prepares progenitor cells for later differentiation

2023-12-05 | GSE227886 | GEO

RNA-seq comparing WT to HDAC3 and Dax1 knock-out clones in cell-sorted populations in 2iLIF and SL(RA) differentiation conditions

Project description:In order to determine the transcriptomic profiles of PrE-induced cells following HDAC3 or Dax1 knock-out in SL(RA) differentiation conditions, RNA-seq was performed on Gata6+ or Nanog+ sort-selected cells. Profiles are contrasted with WT cells in the same differentiation conditions as well as to mock-sorted populations of the three genotypes in 2iLIF conditions.

2021-03-15 | E-MTAB-10150 | biostudies-arrayexpress

Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming.

Project description:Epiblast cells in the early post-implantation stage mammalian embryo undergo a transition described as lineage priming before cell fate allocation, but signaling pathways acting upstream remain ill defined. Genetic studies demonstrate that Smad2/3 double-mutant mouse embryos die shortly after implantation. To learn more about the molecular disturbances underlying this abrupt failure, here we characterized Smad2/3-deficient embryonic stem cells (ESCs). We found that Smad2/3 double-knockout ESCs induced to form epiblast-like cells (EpiLCs) display changes in naive and primed pluripotency marker gene expression, associated with the disruption of Oct4-bound distal regulatory elements. In the absence of Smad2/3, we observed enhanced Bmp target gene expression and de-repression of extra-embryonic gene expression. Cell fate allocation into all three embryonic germ layers is disrupted. Collectively, these experiments demonstrate that combinatorial Smad2/3 functional activities are required to maintain distinct embryonic and/or extra-embryonic cell identity during lineage priming in the epiblast before gastrulation.

| S-EPMC6113931 | biostudies-literature

Derivation of porcine extra-embryonic endoderm cell lines reveals distinct signaling pathway and multipotency states

Project description:We detected the gene expression differences between porcine extra-embryonic endoderm cells and naïve like and primed porcine ESCs. Gene expression of porcine extra-embryonic endoderm cells was distinct with porcine naïve like and primed embryonic stem cells. Pearson correlation analysis confirmed that porcine naïve like and primed ESCs have stronger correlation than the correlation between either pXEN cells and porcine naïve like ESCs or primed ESCs. Porcine extra-embryonic endoderm cells have a distinct identity, clustering neither with porcine naïve like ESCs nor with primed ESCs. We confirmed that porcine extra-embryonic endoderm cells lack the expression of key pluripotency genes, such as Sox2, Pou5f1 and Klf4, but they expressed other pluripotency genes, such as Sall4, Lin28a and Klf5. Furthermore, porcine extra-embryonic endoderm cells robustly express Gata4, Gata6 and Sox17 as well as genes encoding ExEn-associated cell surface proteins or basement membrane components Pdgfra, Col4a2, Lama1, Lamb1, Sparc, Ihh, Hnf4a and Dab2, which is in contrast to porcine naïve like ESCs that express these genes at a low level or lack expression altogether

2021-12-01 | GSE183270 | GEO

Transcription Factor Co-Expression Mediates Lineage Priming for Embryonic and Extra-Embryonic Differentiation

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-12-05 | GSE227889 | GEO

Combinatorial Smad2/3 Activities Downstream of Nodal Signaling Maintain Embryonic/Extra-Embryonic Cell Identities during Lineage Priming

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-08-14 | GSE110164 | GEO

Genome stability in different mouse embryonic stem cells

Project description:Naïve mouse ESCs exhibit full term developmental competence thus hold great potential in regenerative medicine. Maintaining genome stability is essential for potential application of ESCs in stem cell therapy. While ESC potency fluctuate with retrovirus activity, it is unclear whether long-term cultures affect retrotransposition and genomic stability. We compared retrotransposons in naïve ESCs using various approaches. We show that feeder-serum based culture conditions and small molecule LCDM maintain appropriate expression of retrovirus activity following long-term cultures, whereas cultures under 2iLif and a2i result in aberrant upregulation of retrotransposons. This leads to high frequent retrotransposition. Moreover, naïve ESCs on feeder-serum based culture conditions and small molecule LCDM still generate complete ESC pups by TEC assay, functional test of pluripotency, following long-term cultures, despite that all culture conditions maintain high expression levels of pluripotent genes such as Oct4, Nanog, Klf4 and Sox2. Meanwhile, long telomeres are maintained in ESCs under cultures in Feeder-serum and LCDM conditions but telomeres shortened in other conditions with increasing passages. These data provide insights into retrotransposition, genomic stability and pluripotency of naïve ESCs.

2023-09-12 | GSE157874 | GEO

Derivation and characterization of chimera-competent eXtra-Embryonic eNdoderm (XEN) cells from pig blastocysts

Project description:We report for the first time, the derivation and characterization of extra-embryonic endoderm (XEN) cells from primitive endoderm (PrE) of porcine (p) embryos. The pXEN cells can be reliably and reproducibly generated from parthenogenic, in vitro or in vivo derived embryos, and express canonical PrE or XEN cell genes (GATA4, GATA6, SOX17, SALL4, FOXA2, and HNF4A). Transcriptome analysis of pXEN cells revealed close resemblance to yolk sac than any other embryonic or extraembryonic tissue. When introduced into blastocyst stage embryo, the pXEN cells contributed to wide-spread chimerism including visceral yolk sac, chorion, as well as embryonic gut and liver primordium in the fetus. The pXEN cells were shown to be an efficient nuclear donor for generating cloned offspring. Taken together, pXEN cells fulfil a longstanding need for a stable, chimera-competent, and nuclear transfer-compatible porcine embryonic cells with applications for genome editing in livestock.

2019-10-01 | GSE128149 | GEO

Rapid redistribution and extensive cobinding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [reChIP]

Project description:Establishment of divergent cell types from a common progenitor requires transcription factors (TFs) to promote lineage-restricted transcriptional programs while suppressing alternative fates. In the mouse blastocyst, cells of the inner cell mass (ICM) coexpress NANOG and GATA6, two TFs that drive the bifurcation of these progenitors into either the epiblast (Epi) or the primitive endoderm (PrE), respectively. Here, using in vitro differentiation, we describe the molecular mechanisms of how GATA6 quickly induces the PrE fate while repressing the Epi lineage. GATA6 functions as a pioneer TF by inducing nucleosome repositioning at regulatory elements controlling PrE genes, making them accessible for deposition of active histone marks and leading to rewiring of chromatin interactions and ultimately transcriptional activation. GATA6 also binds most regulatory elements of Epi genes followed by eviction of the Epi-specific TFs NANOG and SOX2, loss of active histone marks, and reduction in chromatin accessibility that culminates in transcriptional repression. Unexpectedly, evicted NANOG and SOX2 transiently bind PrE regulatory elements occupied by GATA6. Our study shows that GATA6 binds and modulate the same regulatory elements as Epi TFs, a phenomenon we also validated in blastocysts. We propose that the ability of PrE and Epi-specific TFs to extensively bind and regulate the same gene networks contributes to ICM plasticity and allows rapid cell lineage specification by coordinating both activation and repression of divergent transcriptional programs.

2022-01-16 | GSE193738 | GEO

Rapid redistribution and extensive co-binding of NANOG and GATA6 at shared regulatory elements underlie specification of divergent cell fates [ChIP-seq]

2021-07-30 | GSE181097 | GEO