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Changes in chromatin accessibilityof chondrocytes identified by ATAC-seq in vitro

ABSTRACT: Changes in chromatin accessibilityof chondrocytes identified by ATAC-seq in vitro

PROVIDER: PRJNA1127619 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29528675_1.fastq.gz	Fastqsanger.gz
	SRR29528675_2.fastq.gz	Fastqsanger.gz
	SRR29528676_1.fastq.gz	Fastqsanger.gz
	SRR29528676_2.fastq.gz	Fastqsanger.gz
	SRR29528677_1.fastq.gz	Fastqsanger.gz

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Changes in chromatin accessibilityof chondrocytes identified by ATAC-seq in vitro

Project description:Chromatin accessibility change of chondrocytes in vitro remains unclear. We performed ATAC-seq of P1,P3, and P6 cells in vitro to explore chromatin accessibility change.

2025-06-16 | GSE270644 | GEO

Regularity of Chondrocyte Phenotypic Changes Identified by Single-cell Sequencing in vitro

Project description:The specific mechanism of phenotypic change of chondrocytes in vitro remains unclear. We performed single-cell sequencing of P1,P3, and P6 cells in vitro to explore the mechanisms involved.

2025-06-16 | GSE270642 | GEO

Changes in DNA methylation accompany changes in gene expression during chondrocyte hypertrophic differentiation in vitro.

Project description:BACKGROUND: During osteoarthritis (OA), articular chondrocytes undergo phenotypic changes that resemble developmental patterns characteristic of growth plate chondrocytes. These phenotypic alterations lead to a hypertrophy-like phenotype characterized by altered production of extracellular matrix constituents and increased collagenase activity, which in turn results in cartilage destruction in OA disease. PURPOSE: To identify transcriptomic and epigenomic changes in murine primary articular chondrocytes undergoing hypertrophy-like differentiation in vitro. METHODS: We paired an in vitro 3D/pellet culture system that mimics chondrocyte hypertrophy with RNA sequencing (RNA-Seq) and enhanced reduced representation of bisulfite sequencing (ERRBS). RESULTS: We identified hypertrophy-associated changes in DNA methylation patterns in vitro. Integration of RNA-Seq and ERRBS datasets identified associations between changes in methylation and gene expression. CONCLUSION: Our integrative analyses showed that hypertrophic differentiation of articular chondrocytes is accompanied by transcriptomic and epigenomic changes in vitro.

2020-10-01 | GSE154949 | GEO

In vitro effect of the integrine LAMA4 on motility and cluster formation of human chondrocytes

Project description:Background: Cluster formation of hypertrophic chondrocytes is a sign of late stage osteoarthritis. In vitro chondrocytes have the ability to migrate on scaffolds. Important for motility issues in cartilage are integrines, part of the extracellular matrix, important for locomotory stimuli. The integrine Laminin4 is highly present in hypertrophic clusters of chondrocytes. We were interested if a blockade of LAMA4 is leading to less cluster formation. Methods: Human chondrocytes were cultured in a 2D matrixgel model and treated with different concentrations of a monoclonal anti-LAMA4-antibody.Migration habits were analysed using the cellobserver technique. An array analysis was performed before and after anti-LAMA4 treatment. The data set was screened for possible motility relevant genes. F-actin staining was performed to document cytoskeletal changes. Results: Anti-LAMA4 treatment reduced significantly the rate of cluster formation in human chondrocytes. Cells changed their surface promoting fewer extensions. Genes for motility and migration associated processes were differentially expressed by anti-LAMA4 treatment. Conclusion: LAMA4 blockade leads to less cluster formation in human chondrocytes in vitro. Anti-LAMA4 treatment suppresses filopodia expression, a possible explanation for less clustering. Interestingly anti-LAMA4 treatment seams to support a more milieu of earlier OA human chondrocytes were analysed untreated, IL-1 treated and 2A3 antibody treated

2015-12-22 | E-GEOD-68428 | biostudies-arrayexpress

In vitro effect of the integrine LAMA4 on motility and cluster formation of human chondrocytes

2015-12-22 | GSE68428 | GEO

Regularity of Chondrocyte Phenotypic Changes Identified by Single-cell Sequencing in vitro

Project description:Regularity of Chondrocyte Phenotypic Changes Identified by Single-cell Sequencing in vitro

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The regulatory mechanism of Serinc5 expression in chondrocytes [ATAC-seq]

Project description:The regulatory mechanism of Serinc5 expression in chondrocytes [ATAC-seq]

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Regulatory mechanism of Sox9 gene expression in chondrocytes [ATAC-seq]

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Genome-wide maps of chromatin state in in vivo- and in vitro-derived chondrocytes

Project description:Genome-wide maps of chromatin state in in vivo- and in vitro-derived chondrocytes

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The regulatory mechanism of Serinc5 expression in chondrocytes [ATAC-seq]

Project description:Chondrocytes undergo a series of sequential differentiation steps which result in the formation of a unique hierarchical columnar structure including proliferating, pre-hypertrophic and hypertrophic chondrocytes. Pre-hypertrophic chondrocytes, which exist in the transitional stage between proliferating and hypertrophic chondrocytes, are a rare cell population in the growth plate but critical for endochondral bone development. However, the molecular basis of pre-hypertrophic chondrocytes largely remains elusive. The purpose of this study is to identify novel marker gene and uncover regulatory mechanism of marker gene expression.

2024-11-21 | GSE271633 | GEO

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