Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [ncRNA-Seq]

ABSTRACT: Plants can regenerate entire organs from somatic cells, offering a powerful system to uncover fundamental principles of cellular reprogramming and self-organization. Unlike animals, depending on pre-existing stem cell niches, plants re-establish pluripotency de novo. Although current understanding emphasizes hormonal control and external environmental cues, a unifying framework that explains how millions of cells coordinate fate decisions across space and time remains elusive. Here, we construct a million-cell spatial transcriptomic atlas of plant regeneration, achieving mesoscale resolution observation for all stages of tomato callus development. This atlas reveals a tripartite stem cell niche architecture: an outer signaling layer, intermediate plastic zone, and a quiescent core, features reminiscent of animal regenerative niches. We uncover a fundamental Inducer-Maintainer-Trigger (IMT) triad model, wherein PI-2 (Inducer) establishes a stem cell activating microenvironment, DCL2/22-nt siRNAs (Maintainer) safeguard pluripotency through post-transcriptional regulation, and EPFL8 (Trigger) initiates stem cell niche establishment. This triad model unifies niche signaling, small RNA-mediated plasticity, and metabolic-state-dependent activation, drawing parallels between plant and animal regeneration. Beyond resolving key questions in plant biology, our findings highlight deep evolutionary convergence in regenerative logic across multicellular life, offering new blueprints for engineering regeneration in synthetic biology, crop science, and tissue engineering.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE293046 | GEO | 2026/03/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [scRNA-Seq]

Project description:Plants can regenerate entire organs from somatic cells, offering a powerful system to uncover fundamental principles of cellular reprogramming and self-organization. Unlike animals, depending on pre-existing stem cell niches, plants re-establish pluripotency de novo. Although current understanding emphasizes hormonal control and external environmental cues, a unifying framework that explains how millions of cells coordinate fate decisions across space and time remains elusive. Here, we construct a million-cell spatial transcriptomic atlas of plant regeneration, achieving mesoscale resolution observation for all stages of tomato callus development. This atlas reveals a tripartite stem cell niche architecture: an outer signaling layer, intermediate plastic zone, and a quiescent core, features reminiscent of animal regenerative niches. We uncover a fundamental Inducer-Maintainer-Trigger (IMT) triad model, wherein PI-2 (Inducer) establishes a stem cell activating microenvironment, DCL2/22-nt siRNAs (Maintainer) safeguard pluripotency through post-transcriptional regulation, and EPFL8 (Trigger) initiates stem cell niche establishment. This triad model unifies niche signaling, small RNA-mediated plasticity, and metabolic-state-dependent activation, drawing parallels between plant and animal regeneration. Beyond resolving key questions in plant biology, our findings highlight deep evolutionary convergence in regenerative logic across multicellular life, offering new blueprints for engineering regeneration in synthetic biology, crop science, and tissue engineering.

2026-04-15 | GSE293946 | GEO

Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [spatial]

2026-04-15 | GSE293948 | GEO

Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [RNA-Seq 2]

2026-04-15 | GSE293947 | GEO

Spatially organizing million callus cells identify the core-network enable tomato shoot regeneration [RNA-Seq]

2026-03-27 | GSE292970 | GEO

Synergistic, context-dependent and hierarchical functions of hematopoietic progenitor niche components.

Project description:Specialized niche environments specify and maintain stem and progenitor cells, but little is known about the identities and functional interactions of niche components in vivo. Here, we describe a modular system for the generation of artificial hematopoietic niches in the mouse embryo. A circumscribed tissue that lacks niche function but is physiologically accessible for hematopoietic progenitor cells is functionalized by individual and combinatorial expression of four factors, the chemokines Ccl25 and Cxcl12, the cytokine Scf and the Notch ligand DLL4. The distinct phenotypes and variable numbers of hematopoietic cells in the resulting niches reveal synergistic, context-dependent and hierarchical interactions among niche effector molecules. The surprisingly simple rules determining niche outcomes enable the in vivo engineering of artificial niches conducive to the presence of distinct myeloid or T or B lymphoid lineage precursors. The dataset comprises 24 samples divided into eight sample groups each representing a different lymphoid progenitor cell type isolated from wild-type (+/-) or transgenic (-/-) thymic niches. -/-, Foxn1-deficient genotype; +/-, Foxn1 heterozygous phenotype; DP, CD4/CD8 double-poisztive thymocytes; DN3, CD4/CD8-negative stage 3 thymocytes; SP4, CD4 single-positive thymocytes; SP8, CD8 single-positive thymocytes; B IgM-, IgM surface negative B cells; B IgM+, IgM surface positive B cells; B IgM- -/-, IgM surface negative B cells from Foxn1-deficient genotype.

2012-08-24 | E-GEOD-33268 | biostudies-arrayexpress

Synergistic, context-dependent and hierarchical functions of hematopoietic progenitor niche components.

2012-08-24 | GSE33268 | GEO

RNA-Seq of single cells from regenerating Arabidopsis root

Project description:Plant roots can regenerate after complete excision of their tip, including the stem cell niche, but it is not clear what developmental program mediates such repair. Here, we use a combination of lineage tracing, single-cell RNA-seq, and marker analysis to test different models of tissue reassembly. We show that rapid cell-identity transitions lead to the formation of a new stem cell niche from multiple remnant tissues. The transcriptome of regenerating cells prior to stem cell activation resembled that of the embryonic root progenitor, and regeneration defects were more severe in embryonic versus adult root mutants. Furthermore, the signaling domains of the hormones auxin and cytokinin mirrored their embryonic dynamics, and manipulation of both hormones altered the position of new tissues and stem cell niche markers. Our findings suggest that plant organ regeneration resembles the developmental stages of embryonic patterning and is guided by spatial information laid down by complementary hormone domains. 215 single cells isolated from marked stele tissue (either using WOL or AHP6 promoters), before, at 3h, 16h and 46h post root tip decapitation

2016-04-01 | E-GEOD-74488 | biostudies-arrayexpress

Niche stiffening compromises stem cell potential during aging by reducing chromatin accessibility at bivalent promoters

Project description:Tissue homeostasis and regeneration require activation and subsequent lineage commitment of tissue-resident stem cells (SCs). These state changes are controlled by epigenetic barriers. Using hair follicle stem cells (HFSCs) as paradigm, we studied how aging impacts the chromatin landscape and function of mammalian SCs. Analyses of genome-wide chromatin accessibility revealed that aged HFSCs displayed widespread reduction of chromatin accessibility specifically at key SC self-renewal and differentiation genes that were characterized by bivalent promoters carrying both activating and repressive chromatin marks. Consistently, aged HFSCs showed reduced self-renewing capacity and attenuated ability to activate expression of these bivalent genes upon regeneration. These functional defects were niche-dependent as transplantation of aged HFSCs into young recipients or into ex vivo niches restored SC functions and transcription of poised genes. Mechanistically, aged HFSC niche displayed wide-spread alterations in extracellular matrix composition and mechanics, resulting in compressive forces on SCs and subsequent transcriptional repression, leading to loss of bivalent promoters. Tuning tissue mechanics both in vivo and in vitro recapitulated age-related SC changes, implicating niche mechanics as a central regulator of genome organization and function leading to age-dependent SC exhaustion.

2021-05-07 | PXD018352 | Pride

N-cadherin expressing bone and marrow stromal progenitor cells maintain reserve hematopoietic stem cells

Project description:Regulation of hematopoietic stem cells (HSCs) by bone marrow (BM) niches has been extensively studied; however, whether and how HSC subpopulations are distinctively regulated by BM niches remain unclear. Here, we functionally distinguished reserve HSCs (rHSCs) from primed HSCs (pHSCs) based on their response to chemotherapy and examined how they are dichotomously regulated by BM niches. Both pHSCs and rHSCs supported long-term hematopoiesis in homeostasis; however, pHSCs were sensitive but rHSCs were resistant to chemotherapy. Surviving rHSCs restored the HSC pool and supported hematopoietic regeneration after chemotherapy. The rHSCs were preferentially maintained in the endosteal region that enriches N-cadherin+ (Ncad+) bone-lining cells in homeostasis and post-chemotherapy. N-cad+ cells were functional bone and marrow stromal progenitor cells (BMSPCs), giving rise to osteoblasts, adipocytes, and chondrocytes in vitro and in vivo. Finally, ablation of Ncad+ niche cells or deletion of SCF from N-cad+ niche cells impaired rHSC maintenance during homeostasis and regeneration.

2019-01-15 | GSE104887 | GEO

RNA-Seq of single cells from regenerating Arabidopsis root

2016-04-01 | GSE74488 | GEO