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Resolving Cellular Equipotency of Developing Optic Vesicles

ABSTRACT: The single-cell transcriptomics of PP progenitors revealed the stochastic characteristic of gene expression.

ORGANISM(S): Danio rerio

PROVIDER: GSE114413 | GEO | 2026/05/31

REPOSITORIES: GEO

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Resolving Cellular Equipotency of Developing Optic Vesicles

Project description:Resolving Cellular Equipotency of Developing Optic Vesicles

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Smarcc1 drives optic stalk patterning and optic nerve head astrocyte differentiation

Project description:The optic nerve develops from the neuroectodermal optic stalk, which undergoes coordinated morphogenesis and gives rise to optic nerve astrocytes that support retinal ganglion cell (RGC) axons. Here, we define the progression of astrocyte formation from the optic stalk and identify stage‑specific functions of the SWI/SNF scaffolding subunits Smarcc1 (Baf155) and Smarcc2 (Baf170). Both factors are co‑expressed in retinal pigment epithelium (RPE) and optic stalk progenitors, with Smarcc2 persisting in differentiated RPE and astrocytes. Conditional deletion using Dct‑Cre revealed compensatory activity in pigmented lineages, whereas Smarcc1 loss uniquely disrupted optic nerve head (ONH) morphogenesis, resulting in glial lamina collapse, RGC degeneration, and progressive visual decline. Spatial transcriptomics and functional assays show that Smarcc1 enables dorsal optic stalk progenitors to transition from a pigmented, RPE‑like state to astrocyte progenitors by repressing pigment gene programs and permitting Pax2/Sox2 activity. After specification, Smarcc1 is also required for glial lamina assembly and astrocyte migration into the inner retina. These findings demonstrate that Smarcc1‑dependent chromatin remodeling coordinates astrocyte specification with ONH morphogenesis to maintain long‑term retinal function.

2026-06-29 | GSE336951 | GEO

Fibroblastic reticular cell lineage convergence in Peyer’s patches governs intestinal homeostasis

Project description:Peyer`s patches (PP) are underpinned by a dense network of FRCs. To elaborate the subset composition and topological organization of PP FRCs, we employed well-characterized Ccl19-Cre and Col6a1-Cre mouse models that permit FRC targeting in secondary lymphoid organs. To define PP FRC subsets and their relation to the observed FRC lineages, we isolated fibroblasts from Col6a1Eyfp and Ccl19Eyfp PPs and performed droplet-based single cell transcriptomics analysis. Taken together, the molecular definition of the PP FRC landscape reveals two FRC lineages furnishing distinct microenvironmental niches.

2021-01-22 | E-MTAB-9162 | biostudies-arrayexpress

Camellia oleifera meal peptides alleviates atherosclerosis by regulating lipid metabolism through AMPK/ACC/CPT-1 pathway

Project description:Background: The potential of Camellia oleifera meal peptides（PP) in the treatment of atherosclerosis and its potential mechanism need to be further clarified. Objective: the aim of this study was to clarify the effect of PP in the treatment of atherosclerosis and its potential mechanism. Methods: After cell modeling, it was used to detect the antioxidant, anti-inflammatory and lipid-lowering effects of PP in vitro. As mouse model was used to evaluate the anti atherosclerotic effect of PP in vivo. The changes of protein and metabolites after the treatment of atherosclerosis by PP were studied by liver proteomics, metabonomics and transcriptomics, and the possible mechanism of its regulation of lipid metabolism was clarified. Results:Using cell inflammation model, oxidative damage model and high-fat model, CCK8 test and qPCR detection showed that PP had antioxidant, anti-inflammatory and lipid-lowering effects. The animal results showed that the lipid deposition in the root of aortic valve and liver tissue was reduced, and the PP had the effect of alleviating atherosclerosis. Metabonomics and proteomics analysis showed that the activities of various enzymes related to lipid metabolism were changed after PP treatment, and the lipid metabolism pathway was changed. Transcriptomics analysis showed that AMPK pathway was changed. The experimental results showed that AMPK regulated lipid oxidation pathway to alleviate atherosclerosis in mice through acetyl CoA carboxylase (ACC) - CPT-1 pathway.

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ena-DATASET-WTCHG-10-10-2017-09:37:07:358-646 - samples

Project description:RNA-seq data obtained from directed differentiation of a subset of FiPSCs and BiPSCs cell lines towards islet-like cells. RNA was collected at two key developmental stages: definitive endoderm (DE) and pancreatic progenitors (PP).

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Resolving medulloblastoma cellular architecture by single-cell genomics.

Project description: Not available

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Project description:Full protein measurements from in vitro differentiation of the human embryonic stem cell line HUES8 into pancreatic progenitors (PP) and pancreatic duct-like organoids (PDLOs). Protein intensities were quantified by mass spectrometry analysis from PPs at day 13 and from PDLOs at day 59. Please see related publication “Modelling Plasticity and Dysplasia of Pancreatic Ductal Organoids Derived from Human Pluripotent Stem Cells” for experimental details.

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Project description:Expression of whole retina after optic nerve crush. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0004847

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Gene expression data of Peyer's patch conventional dendritic cells and macrophages at steady state and under TLR7 ligand stimulation

Project description:The initiation of the mucosal immune response in Peyer’s patch (PP) relies on the sampling, processing and efficient presentation of foreign antigens by dendritic cells (DC). PP DC encompass five subsets, among which CD11b+ conventional DC (cDC) and LysoDC have distinct progenitors and functions but share many cell surface markers. This has previously led to confusion between these two subsets. In addition, another PP DC subset, termed double-negative (DN), remains poorly characterized. Here, we have studied the genetic relatedness of the different subsets of PP cDC at steady state and under TLR7 ligand stimulation. We also provide the transcriptional profiles of subepithelial TIM-4- and interfollicular TIM-4+ macrophages.

2017-03-21 | GSE94380 | GEO

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