Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-35166
PROVIDER: PRJNA150799 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report the application of laser capture microdissection (LCM) for high resolution transcriptome profiling of the second internode of the Arabidopsis thaliana inflorescence stem. In this series, we used LCM to determine and compare the transcriptome profiles of the phloem cap, the pith, and the remaining vascular bundle area.
2020-02-10 | GSE142033 | GEO
Project description:Background: Frontal fibrosing alopecia (FFA) is a primary cicatricial alopecia characterised by progressive follicular fibrosis and irreversible hair loss. Despite increasing clinical recognition, the cellular mechanisms sustaining disease persistence remain incompletely defined. Objectives: To define cell-type–specific transcriptional states and inter-compartmental signalling networks in lesional scalp from patients with FFA using single-cell RNA sequencing. Methods: Single-cell RNA sequencing was performed on lesional scalp biopsies from patients with FFA (n = 4) and matched control samples (n = 4). Cells were annotated into major lineages and refined subpopulations, and functional programmes and ligand–receptor-mediated communication were analysed. Results: Analysis of 38,984 high-quality cells revealed preservation of overall cellular composition and lineage architecture in FFA compared with controls. Despite this stability, marked disease-associated transcriptional reprogramming was observed across epithelial, immune and stromal compartments. Keratinocytes retained compartment-specific identity but exhibited prominent activation of stress-response and inflammatory pathways, particularly within upper follicle and bulge/outer root sheath populations. Dermal fibroblasts aligned along a continuous inflammation–fibrosis axis, with relative expansion of inflammatory and ACTA2⁺ states and strengthened coupling between inflammatory and fibrotic programmes. Immune profiling demonstrated skewing of CD4⁺ T cells towards Th1-, Th2- and Th22-associated signatures, together with macrophage reprogramming towards pro-fibrotic, tissue-remodelling states. Ligand–receptor analysis identified TGFB-centred signalling as the dominant inter-compartmental communication axis linking epithelial stress to immune modulation and fibroblast activation. Conclusions: FFA exhibits preserved cellular architecture but extensive, compartment-specific transcriptional reprogramming. Chronic epithelial stress and TGFB-driven inter-compartmental signalling, rather than overt cytotoxic inflammation, emerge as central disease mechanisms.
2026-06-29 | GSE314972 | GEO
Project description:The objective of this study was to identify nutrient-responsive small RNAs in different tissues and in phloem sap of rape plants. miRNA microarrays containing all currently known plant miRNAs (Sanger miRBase versions 10.0, 10.1 and 11.0), and a set of unknown small RNAs cloned earlier from Brassica phloem sap (Bn_PsRNA) were used. The phloem, leaf and root response to nutrient deficiency were analyzed by removing either sulfate, copper or iron from the growth medium. The small RNA profile from phloem and inflorescence stems of plants grown under full nutrition conditions was also analyzed and compared. The study demonstrates that the phloem sap sRNA profile is distinct from that of the inflorescence stems, leaves and roots. Furthermore, we could identify phloem-enriched small RNAs and showed that some of them specifically accumulate in the phloem in response to nutrient deprivation.
2010-02-24 | GSE20263 | GEO
Project description:Transformation of undifferentiated stem cells into cells with special functions is central for organismal development. The phloem tissue mediates long-distance transport of energy metabolites along plant bodies and is characterized by an exceptional degree of cellular specialization. How the phloem-specific developmental program is implemented is, however, unknown. Here we reveal that the ubiquitously expressed PHD-finger protein OBERON3 (OBE3) and the phloem-specific SUPPRESSOR OF MAX2 1-LIKE 5 (SMXL5) protein form a central module for establishing phloem identity in Arabidopsis thaliana (Arabidopsis). By phloem-specific ATAC-seq analyses, we show that OBE3 and SMXL5 proteins establish a phloem-specific chromatin profile.
2021-09-19 | GSE184344 | GEO
Project description:Stems and leaves from 4 week old flax plants were hybridized to an array of cDNAs from the outer (i.e. phloem enriched) layer of stems of the same age to identify transcripts enriched in stem (and phloem bast fibres).
2007-05-01 | E-MEXP-989 | biostudies-arrayexpress
Project description:Cells communicate with each other via receptor-ligand interactions. Here we describe lentiviral-mediated cell e¬ntry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA-sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell-type and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter- vs intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.
2022-12-12 | GSE212996 | GEO
Project description:Cells communicate with each other via receptor-ligand interactions. Here we describe lentiviral-mediated cell e¬ntry by engineered receptor-ligand interaction (ENTER) to display ligand proteins, deliver payloads, and record receptor specificity. We optimize ENTER to decode interactions between T cell receptor (TCR)-MHC peptides, antibody-antigen, and other receptor-ligand pairs. A viral presentation strategy allows ENTER to capture interactions between B cell receptor and any antigen. We engineer ENTER to deliver genetic payloads to antigen-specific T or B cells to selectively modulate cellular behavior in mixed populations. Single-cell readout of ENTER by RNA-sequencing (ENTER-seq) enables multiplexed enumeration of antigen specificities, TCR clonality, cell-type and states of individual T cells. ENTER-seq of CMV-seropositive patient blood samples reveals the viral epitopes that drive effector memory T cell differentiation and inter- vs intra-clonal phenotypic diversity targeting the same epitope. ENTER technology enables systematic discovery of receptor specificity, linkage to cell fates, and antigen-specific cargo delivery.
2022-12-12 | GSE212984 | GEO
Project description:Inter-organellar communication has emerged as a critical factor in maintaining cellular homeostasis under stress conditions. Chloroplasts function not only as central organelles for energy production but are also increasingly recognized as stress sensors and signal integrators. SIGMA FACTOR-BINDING PROTEIN 1 (SIB1), encoded by a nuclear gene, has been identified as a positive regulator of plant immunity, with localization in both chloroplasts and the nucleus. In this study, we identified Arabidopsis SEC23A, a COPII complex component known to mediate membrane trafficking between the endoplasmic reticulum (ER) and the Golgi apparatus, as a novel interactor of SIB1. Our findings reveal that under normal conditions, both SIB1 and SEC23A localize to the ER, while SIB1 is also localized in the nucleus. Upon ER stress and/or treatment with the immunity inducer salicylate, both proteins are relocated from the ER to the chloroplasts. Notably, SEC23A, similar to SIB1, also functions as a positive regulator of disease resistance. In response to pathogen infection, SIB1 and SEC23A downregulate expression of chloroplast- and nucleus-encoded genes associated with photosynthesis while enhancing expression of defense-related genes. Together, our findings reveal a previously uncharacterized pathway of ER–chloroplast communication mediated by SIB1 and SEC23A during plant stress responses and immunity, providing novel insights into the intricate regulatory networks that govern inter-organellar communication under stress in plants.
2026-04-13 | GSE300417 | GEO
Project description:The objective of this study is to analyse the protein composition of A. thaliana phloem at different stages of development. For this purpose phloem exudates have been collected at different time points (vegetative stage, floral transition and reproductive stage).
2026-04-13 | PXD065325 | Pride
Project description:Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor interactions. Targeting ligand-receptor interactions, for instance with immune check-point inhibitors, can provide significant benefit for patients. However, our knowledge of which interactions occur in a tumor and how these interactions affect outcome is still limited. We present an approach to characterize communication by ligand-receptor interactions across all cell types in a microenvironment using single-cell RNA sequencing. We apply this approach to identify and compare ligand-receptor interactions present in six syngeneic mouse tumor models. To identify interactions potentially associated with outcome, we regress interactions against phenotypic measurements of tumor growth rate. In addition, we quantify ligand-receptor interactions between T-cell subsets and their relation to immune infiltration using a publicly available human melanoma data-set. Overall, this approach provides a tool for studying cell-cell interactions, their variability across tumors, and their relationship to outcome.
2018-10-27 | GSE121861 | GEO