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High-Depth Transcriptomic Profiling Reveals the Temporal Gene Signature of Mesenchymal Stem Cells During Chondrogenesis

ABSTRACT: High-Depth Transcriptomic Profiling Reveals the Temporal Gene Signature of Mesenchymal Stem Cells During Chondrogenesis

PROVIDER: PRJNA431247 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6491460_1.fastq.gz	Fastqsanger.gz
	SRR6491460_2.fastq.gz	Fastqsanger.gz
	SRR6491470_1.fastq.gz	Fastqsanger.gz
	SRR6491470_2.fastq.gz	Fastqsanger.gz
	SRR6491461_1.fastq.gz	Fastqsanger.gz

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High-Depth Transcriptomic Profiling Reveals the Temporal Gene Signature of Mesenchymal Stem Cells During Chondrogenesis

Project description:High-Depth Transcriptomic Profiling Reveals the Temporal Gene Signature of Mesenchymal Stem Cells During Chondrogenesis

| PRJNA431247 | ENA

High-Depth Transcriptomic Profiling Reveals the Temporal Gene Signature of Mesenchymal Stem Cells During Chondrogenesis

Project description:Cartilage tissue engineering seeks to replace degenerated or damaged cartilage following disease or injury. Mesenchymal stem/stromal cells (MSCs) provide an attractive cell source for cartilage repair; however, the underlying molecular pathways that drive chondrogenesis of these pools of adult stem cells remains poorly understood. Here, we generated a rich data set of high throughput RNA sequencing of human MSCs throughout chondrogenesis at six different time points. Our data is consisted of 18 libraries with three individual donors as biological replicates, each library possessing a sequencing depth of 100 million reads. We also performed flow cytometric, histological, and biochemical analyses in parallel to validate the quality of our in vitro engineered cartilage. Differential gene expression and gene ontology analyses identified dynamic changes in multiple biological pathways, namely downregulation in cell cycle and proliferation, and upregulation in extracellular matrix synthesis. Weighted gene correlation network analysis also identified an important chondrogenic gene subset, whose functional characterization promises to further harness the potential of MSCs for cartilage tissue engineering. Furthermore, we created a graphic user interface encyclopedia built with the goal of producing an open resource of transcriptomic regulation for additional data-mining and pathway analysis of the process of MSC chondrogenesis. The tool can be accessed at: http://msc-browser.guilaklab.com

2018-07-11 | GSE109503 | GEO

High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis.

Project description:Mesenchymal stem/stromal cells (MSCs) provide an attractive cell source for cartilage repair and cell therapy; however, the underlying molecular pathways that drive chondrogenesis of these populations of adult stem cells remain poorly understood. We generated a rich data set of high-throughput RNA sequencing of human MSCs throughout chondrogenesis at 6 different time points. Our data consisted of 18 libraries with 3 individual donors as biologic replicates, with each library possessing a sequencing depth of 100 million reads. Computational analyses with differential gene expression, gene ontology, and weighted gene correlation network analysis identified dynamic changes in multiple biologic pathways and, most importantly, a chondrogenic gene subset, whose functional characterization promises to further harness the potential of MSCs for cartilage tissue engineering. Furthermore, we created a graphic user interface encyclopedia built with the goal of producing an open resource of transcriptomic regulation for additional data mining and pathway analysis of the process of MSC chondrogenesis.-Huynh, N. P. T., Zhang, B., Guilak, F. High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis.

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Characterisation of DNA methylation during mesenchymal stem cell chondrogenesis

Project description:Characterisation of DNA methylation during mesenchymal stem cell chondrogenesis

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Human bone-marrow-derived mesenchymal stem cells: control vs. cells undergoing chondrogenesis

Project description:Long non-coding RNAs profiling of human mesenchymal stem cells comparing undifferentiated HMSCs with differentiated HMSCs during chondrogenesis. The chondrogenic differentiation of HMSCs was induced by chondrogenic medium. The chondrogenic marker genes (Col2a1, Sox9 and ACAN) has been detected upregulating during this process by Q-PCR. The aim of this study is to determine key lncRNAs regulating the chondrogenic differentiation process.

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Characterisation of DNA methylation during mesenchymal stem cell chondrogenesis

Project description:Regulation of transcription occurs in a cell type specific manner orchestrated by epigenetic mechanisms including DNA methylation. Methylation changes may also play a key role in lineage specification during stem cell differentiation. To further our understanding of epigenetic regulation in chondrocytes we characterised DNA methylation changes during chondrogenesis of mesenchymal stem cells (MSCs) by Infinium 450K methylation array. Significant DNA hypomethylation was identified during chondrogenesic differentiation including changes at many key cartilage gene loci. Integration with chondrogenesis gene expression data revealed an enrichment of significant CpGs in upregulated genes, while characterisation of significant CpG loci indicated their predominant localisation to enhancer regions. Comparison with methylation profiles of other tissues, including healthy and diseased adult cartilage, identified chondrocyte-specific regions of hypomethylation and the overlap with differentially methylated CpGs in osteoarthritis. Taken together we have associated DNA methylation levels with the chondrocyte phenotype. The consequences of which has potential to improve cartilage generation for tissue engineering purposes and also to provide context for observed methylation changes in cartilage diseases such as osteoarthritis

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