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 identifies Atf3+ senescent chondrocytes in the aged rat meniscus

ABSTRACT: Single-cell RNA sequencing identifies Atf3+ senescent chondrocytes in the aged rat meniscus

PROVIDER: PRJNA1207524 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA sequencing identifies Atf3+ senescent chondrocytes in the aged rat meniscus

Project description:we conducted single-cell RNA sequencing (scRNA-seq) analysis using the 10x Chromium platform to uncover the cellular composition and molecular profiles of meniscal cells from different age groups.The meniscus, a fibrocartilaginous structure essential for joint load distribution, is highly susceptible to age-related degeneration. With aging, the meniscus experiences structural and functional deterioration, contributing to the progression of osteoarthritis(OA). This study aims to bridge this gap by profiling the cellular landscape and analyzing age-related changes in the aging meniscus using scRNA-seq.

2025-01-14 | GSE286034 | GEO

Aging attenuates the infrapatellar fat pad’s paracrine capacity to promote extracellular matrix production in aged chondrocytes

Project description:Objective: To elucidate the age and sex-specific impact of the IFP secretome on aged chondrocytes, and uncover the exact mechanism driving these effects. To explore mediators of the IFP on chondrocytes, we performed mass-spectrometry proteomics of CM from young versus aged male IFP and mass spectrometry on aged male chondrocytes treated with CM of the same experimental groups. Network analysis interrogated age-dependent changes in communication between IFP-derived secreted proteins and chondrocytes. Results: Col2 and aggrecan expression were significantly increased in chondrocytes co-cultured with young IFP tissue compared to aged IFP tissue, and young CM compared to aged CM. There was no significant increase in SOX9 under any of the different conditions. Similar trends were seen in female experiments. Multi-omics results combined with network analysis suggested IFPs secrete succinate co-A ligase related factors that regulate Hox-dependent spliceosome gene expression in chondrocytes in an age-dependent manner. Conclusions: This study suggests that a young IFP secretome enhances ECM production by aged chondrocytes, in part through enhanced mitochondrial activity. However, this beneficial effect decreases with age.

2024-12-31 | GSE264710 | GEO

Integrated Analysis of lncRNA and mRNA Expression Profiles Indicates Age-related Changes in Meniscus

Project description:Little has been known about the role of long non-coding RNA (lncRNA) involves in meniscus degradation with aging.In order to investigate the molecular mechanisms of age-related meniscal degeneration and further explore potential biologic therapeutic targets, we performed microarray analysis of meniscus to determine lncRNAs and mRNAs expression profiles in young and aging adults. Then, we carried out bioinformatics analysis of differentially expressed molecules to identify key molecules and functional pathways in the aged meniscus tissues.

2022-04-06 | GSE191157 | GEO

Meniscus Gene Expression Profiling: Inner and Outer Zone Tissue Comparison to Cartilage and Passaged Monolayer Meniscus Cells

Project description:Meniscus injuries are common and while surgical strategies have improved, there is a need for alternative therapeutics to improve long-term outcomes and prevent post-traumatic osteoarthritis. Current research efforts in regenerative therapies and tissue engineering are hindered by a lack of understanding of meniscus cell biology and a poorly defined meniscus cell phenotype. This study utilized bulk RNA-sequencing to identify unique and overlapping transcriptomic profiles in cartilage, inner and outer zone meniscus tissue, and passaged inner and outer zone meniscus cells. The greatest transcriptomic differences were identified when comparing meniscus tissue to monolayer cultured cells (> 4,600 differentially expressed genes (DEGs)) and meniscus tissue to cartilage (> 3,100 DEGs). While zonal differences exist within the meniscus tissue (205 DEGs between inner and outer zone meniscus tissue), meniscus resident cells are more similar to each other than to either cartilage or monolayer meniscus cells. Additionally, we identified and validated LUM and PRRX1 as potential markers for meniscus tissue and ACTA2, FSTL1, SFRP2, and TAGLN as novel markers for meniscus cell dedifferentiation. Our data contribute significantly to the current characterization of meniscus cells and provide an important foundation for future work in meniscus cell biology, regenerative medicine, and tissue engineering.

2024-11-10 | GSE275100 | GEO

Gene signature of the embryonic meniscus

Project description:Analysis of gene expression in E16 mouse meniscus, articular cartilage, and cruciate ligaments Limbs were dissected from E16 CD-1 mice. Samples were frozen in OCT and cryosectioned. Meniscus, articular carilage, and cruciate ligament were isolated using laser capture microdissection. Total RNA was isolated from these tissues, amplified, and gene expression was analyzed using microarrays. Three biological replicates were analyzed for each tissue type. Total RNA extracted from E16 mouse meniscus, articular cartilage, and cruciate ligaments

2013-10-01 | E-GEOD-47799 | biostudies-arrayexpress

Single cell-seq identify discoid lateral meniscus

Project description:Discoid lateral meniscus (DLM) is more prone to injury than a normally shaped meniscus. Our previous study successfully identified the different cell types and their corresponding marker genes in meniscus tissues, but there was no study comparing the gene expression and cell heterogenicity of discoid meniscus with normal meniscus.

2023-12-06 | GSE162767 | GEO

Transcriptome Analysis of Human Injured Meniscus Reveals a Distinct Phenotype of Meniscus Degeneration with Aging

Project description:In this study, we have tested the variation in gene expression signatures in human injured meniscus with age and degree of chondrosis in the knee. We found several genes that were differentially regulated with each of these factors and they represent important biological pathways in osteoarthritis research. Total RNA obtained from isolated injured meniscus tissues from patients undergoing arthroscopic partial meniscectomy.

2013-03-18 | E-GEOD-45233 | biostudies-arrayexpress

Single-cell RNA-seq analysis identifies meniscus progenitors and reveals the progression of meniscus degeneration

Project description:We identified seven clusters in healthy human meniscus, including five empirically-defined populations and two novel populations. Pseudotime analysis showed EC and FCP existed at the pseudospace trajectory start. MCAM (CD146) was highly expressed in two clusters. CD146+ meniscus cells differentiated into osteoblasts and adipocytes and formed colonies. We identified changes in the proportions of degenerated meniscus cell clusters and found a cluster specific to degenerative meniscus with progenitor cell characteristics. The reconstruction of four progenitor cell clusters indicated that FCP differentiation into DegP was an aberrant process. Interleukin-1β stimulation in healthy human meniscus cells decreased CD146+ cells and increased CD318+ cells, while TGFβ1 attenuated the increase in CD318+ cells in degenerated meniscus cells.

2020-02-26 | GSE133449 | GEO

Effect of depletion of pre-existing senescent cells in aged hamstrers on gene expression in lungs

Project description:To investigate the potential role of senescent cells in COVID19-like pathology, aged hamsters were treated with the senolytics ABT-263 one day prior to a SARS-CoV-2 infection

2023-05-19 | GSE231673 | GEO

Gene expression profiling of cellular senescence in mouse articular chondrocytes

Project description:mRNA profiles of primary mouse chondrocytes exposed to senescence stress (bleomycin, doxorubicin) or acute inflammation (interleukin-1 beta) were generated by mRNA sequencing. This study provides transcriptome landscape of senescent chondrocytes.

2024-11-11 | GSE281015 | 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