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The temporal transcriptomic signature of cartilage formation

ABSTRACT: The temporal transcriptomic signature of cartilage formation

PROVIDER: PRJEB60592 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11011000.fastq.gz	Fastqsanger.gz
	ERR11011001.fastq.gz	Fastqsanger.gz
	ERR11011002.fastq.gz	Fastqsanger.gz
	ERR11011003.fastq.gz	Fastqsanger.gz
	ERR11011004.fastq.gz	Fastqsanger.gz

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The temporal transcriptomic signature of cartilage formation

Project description:To study chondrogenesis, we used a chicken limb bud model: We used RNA sequencing, and examined the differences between gene expression patterns during cartilage formation in micromass cultures of embryonic limb bud-derived progenitors. We sequenced in triplicate at Day 0,1,2,3,4,6,10,15 and also from mature birds.

2023-03-28 | E-MTAB-12770 | biostudies-arrayexpress

The temporal transcriptomic signature of cartilage formation.

Project description:Chondrogenesis is a multistep process, in which cartilage progenitor cells generate a tissue with distinct structural and functional properties. Although several approaches to cartilage regeneration rely on the differentiation of implanted progenitor cells, the temporal transcriptomic landscape of in vitro chondrogenesis in different models has not been reported. Using RNA sequencing, we examined differences in gene expression patterns during cartilage formation in micromass cultures of embryonic limb bud-derived progenitors. Principal component and trajectory analyses revealed a progressively different and distinct transcriptome during chondrogenesis. Differentially expressed genes (DEGs), based on pairwise comparisons of samples from consecutive days were classified into clusters and analysed. We confirmed the involvement of the top DEGs in chondrogenic differentiation using pathway analysis and identified several chondrogenesis-associated transcription factors and collagen subtypes that were not previously linked to cartilage formation. Transient gene silencing of ATOH8 or EBF1 on day 0 attenuated chondrogenesis by deregulating the expression of key osteochondrogenic marker genes in micromass cultures. These results provide detailed insight into the molecular mechanism of chondrogenesis in primary micromass cultures and present a comprehensive dataset of the temporal transcriptomic landscape of chondrogenesis, which may serve as a platform for new molecular approaches in cartilage tissue engineering.

| S-EPMC10164575 | biostudies-literature

Project description:Transcriptomic signature of cartilage formation

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Transcriptomic signatures of cartilage ageing

Project description:Transcriptomic signatures of cartilage ageing

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Project description:Transcriptomic signature of cartilage formation, extention

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GRNs driving cartilage and bone formation interact via averaging and synergism during cartilage maturation

Project description:GRNs driving cartilage and bone formation interact via averaging and synergism during cartilage maturation

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Dermatomyositis skin transcriptomic signature

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Epiphyseal cartilage

Project description:Chondrocytes from extra fingers exhibited a high proliferative capacity: the cells reached to population doublings (PD) 30-35 within 4 weeks before replicative senescence. The propagated cells formed hyaline cartilage at 2 weeks after subcutaneous implantation of NOD/Scid/IL-2 receptor gamma knock out (NOG) mice, and the generated cartilage showed enchondral ossification at 8 to 12 weeks. The cartilage formation with osteogenesis depends on the number of cell division in vitro. Keywords: NCCH BioResource Affymetrix human U133 plus 2.0 array was used to transcriptionally profile to determine the expression changes in epiphyseal cartilage.

2011-03-22 | E-GEOD-17368 | biostudies-arrayexpress

Transcriptomic signatures of cartilage ageing

Project description:Equine cartilage from young and old donors was used for RNA-Seq analysis. The aim of the study was to identify differentially expressed cartilage transcripts in ageing in order to to characterize molecular mechanisms associated with age-related changes in

2014-01-11 | E-MTAB-1386 | biostudies-arrayexpress

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

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