Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [ST-seq]

ABSTRACT: Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [ST-seq]

PROVIDER: PRJNA1031780 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26495145_1.fastq.gz	Fastqsanger.gz
	SRR26495145_2.fastq.gz	Fastqsanger.gz
	SRR26495146_1.fastq.gz	Fastqsanger.gz
	SRR26495146_2.fastq.gz	Fastqsanger.gz
	SRR26495147_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [ST-seq]

Project description:The bone-defect-repair process involves complex interaction between mesenchymal stem cells (MSCs) and immune cells, while the heterogeneity of osteoimmune microenvironment around implanted biomaterials remains elusive. By combining analysis of scRNA-seq and spatial transcriptomics technologies, we revealed that MgphiMSCs subpopulation served as the pioneers during the early stage of biomaterials-mediated bone defect healing process. They performed efficient osteogenic differentiation potential and had close interactions with immune cells. Remarkably, the MgphiMSCs could response to biomaterials-mediated osteoimmune microenvironment, rewired the polarization and osteoclastic differentiation of macrophages via midkine (MDK) signaling pathway. The inhibition of MDK activated the pro-inflammatory programs of macrophages and osteoclastogenesis. Meanwhile, multiple innate and adaptive immune-cell subsets exhibited close crosstalk between MgphiMSCs via SPP1 signaling pathway. These cellular profiles and interactions characterized in this study could broaden our understanding of the functional MSCs subpopulations at the early stage of biomaterial-mediated bone regeneration and provide the basis for the materials-designed strategies that target osteoimmune modulation.

2024-06-30 | GSE246096 | GEO

Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [scRNA-seq]

2024-06-30 | GSE246475 | GEO

Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration

Project description:Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration

| PRJNA1033176 | ENA

Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [scRNA-seq]

Project description:Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration [scRNA-seq]

| PRJNA1033178 | ENA

Single-cell RNA sequencing and spatial transcriptomics reveal the osteoimmune microenvironment of biomaterial-mediated bone regeneration

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

2024-06-30 | GSE246476 | GEO

The Role of WTAP in Regulating Macrophage-Mediated Osteoimmune Responses and Tissue Regeneration in Periodontitis

Project description:Periodontitis, delineated by the destruction of structures that support teeth, is predominantly propelled by intricate immune responses. Immunomodulatory treatments offer considerable promise for the management of this ailment; however, the modulation of the periodontal immune microenvironment to facilitate tissue regeneration presents a substantial biomedical challenge. Herein, our study investigates the role of Wilms' tumor 1-associating protein (WTAP), a critical m6A methyltransferase, in the immunomodulation of periodontitis and assesses its viability as a therapeutic target. We observed heightened expression of WTAP in macrophages extracted from gingival tissues impacted by periodontitis, with a strong association with M1 polarization. Via loss-of-function experiments, we demonstrated that diminishing WTAP expression precipitates a transition from M1 to M2 macrophage phenotypes amidst inflammatory conditions, thus improving the periodontal immune landscape. Further, RNA sequencing and indirect co-culture assays indicated that suppressing of WTAP expression modulates osteoimmune responses and enhances the osteogenic differentiation of bone marrow stromal cells. The local deployment of adeno-associated virus-shWTAP in murine models of periodontitis robustly validated the therapeutic promise of targeting WTAP in this disease. Collectively, our findings highlight the crucial role of WTAP in orchestrating macrophage-mediated osteoimmune responses and tissue regeneration in periodontitis, proposing novel avenues for immunotherapeutic interventions in its treatment.

2024-05-24 | GSE265968 | GEO

Exosome integrated biomaterial in bone regeneration

Project description:Mineralized osteoblast-derived exosomes integrated on a polysaccharide-protein conjugated biomaterial promote bone regeneration by transferring the regulatory miRNAs

| PRJEB65457 | ENA

Open-ST: High-resolution spatial transcriptomics in 3D

Project description:Spatial transcriptomics (ST) methods unlock molecular mechanisms underlying tissue development, homeostasis, or disease. However, there is a need for easy-to-use, high-resolution, cost-efficient, and 3D-scalable methods. Here, we report Open-ST, a sequencing-based, open-source experimental and computational resource to address these challenges and to study the molecular organization of tissues in 2D and 3D. In mouse brain, Open-ST captured transcripts at subcellular resolution and reconstructed cell types. In primary head-and-neck tumors and patient-matched healthy/metastatic lymph nodes, Open-ST captured the diversity of immune, stromal, and tumor populations in space, validated by imaging-based ST. Distinct cell states were organized around cell-cell communication hotspots in the tumor but not the metastasis. Strikingly, the 3D reconstruction and multimodal analysis of the metastatic lymph node revealed spatially contiguous structures not visible in 2D and potential biomarkers precisely at the 3D tumor/lymph node boundary. All protocols and software are available at https://rajewsky-lab.github.io/openst.

2024-06-23 | GSE251926 | GEO

Mgp High-Expressing MSCs Orchestrate the Osteoimmune Microenvironment of Collagen/Nanohydroxyapatite-Mediated Bone Regeneration.

Project description:Activating autologous stem cells after the implantation of biomaterials is an important process to initiate bone regeneration. Although several studies have demonstrated the mechanism of biomaterial-mediated bone regeneration, a comprehensive single-cell level transcriptomic map revealing the influence of biomaterials on regulating the temporal and spatial expression patterns of mesenchymal stem cells (MSCs) is still lacking. Herein, the osteoimmune microenvironment is depicted around the classical collagen/nanohydroxyapatite-based bone repair materials via combining analysis of single-cell RNA sequencing and spatial transcriptomics. A group of functional MSCs with high expression of matrix Gla protein (Mgp) is identified, which may serve as a pioneer subpopulation involved in bone repair. Remarkably, these Mgp high-expressing MSCs (MgphiMSCs) exhibit efficient osteogenic differentiation potential and orchestrate the osteoimmune microenvironment around implanted biomaterials, rewiring the polarization and osteoclastic differentiation of macrophages through the Mdk/Lrp1 ligand-receptor pair. The inhibition of Mdk/Lrp1 activates the pro-inflammatory programs of macrophages and osteoclastogenesis. Meanwhile, multiple immune-cell subsets also exhibit close crosstalk between MgphiMSCs via the secreted phosphoprotein 1 (SPP1) signaling pathway. These cellular profiles and interactions characterized in this study can broaden the understanding of the functional MSC subpopulations at the early stage of biomaterial-mediated bone regeneration and provide the basis for materials-designed strategies that target osteoimmune modulation.

| S-EPMC11187922 | biostudies-literature

Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics [Nova-ST]

Project description:Spatial transcriptomics workflows using barcoded capture arrays are commonly used for resolving gene expression in tissues. However, existing techniques are either limited by capture array density or are cost prohibitive for large scale atlasing. We present Nova-ST, a dense nano-patterned spatial transcriptomics technique derived from randomly barcoded Illumina sequencing flow cells. Nova-ST enables customized, low cost, flexible, and high-resolution spatial profiling of large tissue sections. Benchmarking on mouse brain sections demonstrates significantly higher sensitivity compared to existing methods, at reduced cost.

2024-02-22 | GSE256318 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data