Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA307195 | ENA |
REPOSITORIES: ENA
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Project description:Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation.
2016-06-23 | GSE76408 | GEO
Project description:Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation. We traced Lgr5+ stem cells from Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice and sorted YFP+ cells 5 days, 3 weeks and 8 weeks after tamoxifen injection.
2016-06-23 | E-GEOD-76408 | biostudies-arrayexpress
Project description:We combined lineage tracing with single cell RNA sequencing (scRNA-seq) to study the mechanisms underlying the conversion of Paneth cells into bona fide tumor cells.
2024-03-27 | GSE221820 | GEO
Project description:Mitochondrial trifunctional protein deficiency, due to mutations in hydratase subunit A (HADHA), results in sudden infant death syndrome (SIDS) with no cure. To reveal the disease etiology, we generated stem cell-derived cardiomyocytes from HADHA-deficient hiPSCs and accelerated their maturation via a novel, engineered MicroRNA Maturation Cocktail (MiMaC) that upregulated the epigenetic regulator, HOPX. Fatty acid challenged MiMaC treated HADHA mutant cardiomyocytes manifested the disease phenotype: defective calcium dynamics and repolarization kinetics which resulted in a pro-arrhythmic state. Single cell RNA-seq revealed a novel cardiomyocyte developmental intermediate, based on metabolic gene expression. This intermediate gave rise to mature-like cardiomyocytes in control cells but, mutant cells transitioned to a pathological state with reduced fatty acid beta-oxidation (FAO), reduced mitochondrial proton gradient, disrupted cristae structure and defective cardiolipin remodeling. This study reveals that TFPa/HADHA, a MLCL-AT-like enzyme, is required for FAO and cardiolipin remodeling, essential for functional mitochondria in human cardiomyocytes.
2019-08-26 | ST001246 | MetabolomicsWorkbench
Project description:Neurogenesis comprises many steps from progenitor proliferation to neuronal differentiation and maturation. These processes are highly regulated, but the landscape of transcriptional changes underlying brain development are poorly characterized. Here, we describe a developmental single-cell RNA-seq catalog of ~220,000 zebrafish brain cells encompassing 12 stages from 12 hours post-fertilization to 15 days post-fertilization. We characterize known and novel gene markers for ~800 clusters and provide an overview of the diversification of neurons and progenitors across these timepoints. We also introduce an optimized version of the GESTALT lineage recorder that enables higher expression and recovery of Cas9-edited barcodes to query lineage segregation. Cell type characterization indicates that most embryonic neural progenitor states are transitory and transcriptionally distinct from neural progenitors of post-embryonic stages. Reconstruction of cell specification trajectories reveals that late-stage retinal neural progenitors transcriptionally overlap cell states observed in the embryo. The zebrafish brain development atlas provides a resource to define and manipulate specific subsets of neurons and to uncover the molecular mechanisms underlying vertebrate neurogenesis.
2020-09-18 | GSE158142 | GEO
Project description:Single-cell RNA-seq reveals distinct subsets of circulating human neutrophils
| PRJNA778206 | ENA
Project description:Pancreatic β and α cells play essential roles in maintaining glucose homeostasis. However, the mechanisms by which these distinct cell populations are generated, expand, and mature during pancreas development remain unclear. In this study, we addressed this critical question by performing a single-cell transcriptomic analysis of mouse β and α cells sorted from fetal to adult stages. We discovered that β and α cells use different regulatory strategies for their maturation and that cell proliferation peaks at different developmental times. However, the quiescent and proliferative cells in both the β lineage and α lineage are synchronous in their maturation states. The heterogeneity of juvenile β cells reflects distinct cell-cycling phases, origins, and maturation states, whereas adult β cells are relatively homogeneous at the transcriptomic level. These analyses provide not only a high-resolution roadmap for islet lineage development but also insights into the mechanisms of cellular heterogeneity, cell number expansion, and maturation of both β and α cells.
2017-05-02 | GSE87375 | GEO
Project description:BACKGROUND & AIMS: Stems cells within the intestinal epithelium generate daughter cells which undergo lineage commitment and maturation through the concerted action of the Wnt and Notch signalling cascades. Both pathways, in turn, regulate transcription factor networks which further define differentiation towards either enterocytes or one of three secretory cell lineages (Paneth, goblet or enteroendocrine cells). In this manuscript, we identified the Ets domain transcription factor, Spdef, as a novel lineage maker of goblet and Paneth cells. METHODS: To address the function of Spdef in vivo, we inactivated the Spdef gene and analysed the intestinal phenotype using a range of histological techniques and DNA microarray profiling. RESULTS: In accordance with the expression data we found that loss of Spdef severely impaired the maturation of goblet and Paneth cells and conversely lead to an accumulation of immature secretory progenitors. Moreover, we provide evidence suggesting that Spdef positively and negatively regulates a specific subset of goblet and Paneth cell genes including Cryptdins, Mmp7, Ang4, Kallikreins, and Muc2. CONCLUSION: We propose a model whereby Spdef acts downstream of Math1 to promote terminal differentiation of a secretory progenitor pool towards Paneth and goblet cells. Keywords: expression profiling
2010-02-10 | GSE14892 | GEO
Project description:We employed marker-free single-cell RNA-Seq to characterize comprehensive transcriptional profiles of 507 cells from seven stages between embryonic day 11.5 and postnatal day 2.5 during mouse liver development. Our data demonstrated the existence of two types of stem/progenitor cells with distinct molecular patterns during liver development. Both types of cells exhibit heterogeneity of transcriptional program within each cell population, suggesting they be in distinct status of self-renewal, cell proliferation and different sub-stages of differentiation and maturation. In general, our data depicting the dynamic trajectories with transcriptional profiles at single-cell resolution during mouse liver development provides insights into the fate decision and transcriptional control of self-renewal, differentiation and maturation of liver stem/progenitor cells.
2017-11-20 | GSE87795 | GEO
Project description:We purified (FACS) and profiled (RNA-Seq) zebrafish embryo skin cells vs. nonskin cells at three early developmental stages. At two of the stages, we further purified and profiled two distinct epithelial layers of the skin: the periderm and basal cells. Our comprehensive expression analysis provides the first reported transcriptomes of these two cell types, reveals gene expression dynamics in space and time, and identifies common and distinct features of epithelial maturation in the two layers. Given the conserved nature of skin development, we believe our study to be of interest to those studying skin in other vertebrates.
2019-08-21 | GSE132304 | GEO