Ontology highlight
ABSTRACT:
PROVIDER: PRJNA817177 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18356364.fastq.gz | Fastqsanger.gz | |||
| SRR18356365.fastq.gz | Fastqsanger.gz | |||
| SRR18356366.fastq.gz | Fastqsanger.gz | |||
| SRR18356367.fastq.gz | Fastqsanger.gz | |||
| SRR18356368.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
Similar Datasets
Project description:The temporal transcriptomic signature of cartilage formation
| PRJEB60592 | ENA
Project description:Osteoarthritis (OA) is a prevalent degenerative disease, which involves progressive and irreversible destruction of cartilage matrix. Despite efforts to reconstruct cartilage matrix in osteoarthritic joints, it has been a difficult task as adult cartilage exhibits marginal repair capacity. Here we report the identification of tankyrase as a regulator of the cartilage anabolism axis based on systems-level factor analysis of mouse reference populations. Tankyrase inhibition drives the expression of a cartilage-signature matrisome and elicits a transcriptomic pattern that is inversely correlated with OA progression. Furthermore, tankyrase inhibitors ameliorate surgically-induced OA in mice, and stem cell transplantation coupled with tankyrase knockdown results in superior regeneration of cartilage lesions. Mechanistically, the pro-regenerative features of tankyrase inhibition are mainly triggered by uncoupling SOX9 from a poly(ADP-ribosyl)ation (PARylation)-dependent protein degradation pathway. Our findings provide insights into the development of future OA therapies aimed at reconstruction of articular cartilage.
2019-09-24 | GSE137899 | GEO
Project description:We used human fetal bone marrow-derived mesenchymal stromal cells (hfMSCs) differentiating towards chondrocytes as an alternative model for the human growth plate (GP). Our aims were to study gene expression patterns associated with chondrogenic differentiation to assess whether chondrocytes derived from hfMSCs are a suitable model for studying the development and maturation of the GP. hfMSCs efficiently formed hyaline cartilage in a pellet culture in the presence of TGFB3 and BMP6. Microarray and principal component analysis were applied to study gene expression profiles during chondrogenic differentiation. A set of 232 genes was found to correlate with in vitro cartilage formation. Several identified genes are known to be involved in cartilage formation and validate the robustness of the differentiating hfMSC model. KEGG pathway analysis using the 232 genes revealed 9 significant signaling pathways correlated with cartilage formation. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development. RNA fhMSCs of chondrogenically differentiating fhMSCs was isolated at week, 0, 1, 2, 3, 4 and 5. Moreover, RNA of 4 human growth plates from was isolated.
2013-04-22 | E-GEOD-40942 | biostudies-arrayexpress
Project description:Craniofacial morphogenesis depends on complex cell fate decisions during the differentiation of post-migratory cranial neural crest cells. Molecular mechanisms of cell differentiation of mesenchymal cells to developing bones, cartilage, teeth, tongue, and other craniofacial tissues are still poorly understood. We performed single-cell transcriptomic analysis of craniofacial mesenchymal cells derived from cranial NCCs in mouse embryo. Using FACS sorting of Wnt1-Cre2 progeny, we carefully map the cell heterogeneity in the craniofacial region during the initial stages of bone and cartilage formation.
2024-10-29 | GSE262468 | GEO
Project description:Hox genes control domain specific cartilage pattern formation along the proximodistal axis. Hoxa11 and Hoxd11 (Hox11) show overlapping expression in the mesenchyme of the zeugopod and regulate cartilage growth and differentiation. Hoxa13 and Hoxd13 (Hox13) are expressed in the autopodal mesenchyme and are crucial for the autopodal cartilage patterning. Since both Hox11 and Hox13 are involved in the limb cartilage development, they may share the target genes. To identify common target genes among the Hoxa11 and Hoxa13, we performed ChIP-Seq analysis using specific antibody.
2019-03-28 | GSE119142 | GEO
Project description:Cartilage pellets generated from ectomesenchymal progeny of human pluripotent stem cells (hPSCs) in vitro eventually show signs of commitment of chondrocytes to hypertrophic differentiation. When transplanted subcutaneously, most of the surviving pellets were fully mineralized by 8 weeks. In contrast, treatment with the adenylyl cyclase activator, forskolin, in vitro resulted in slightly enlarged cartilage pellets containing an increased proportion of proliferating immature chondrocytes that expressed very low levels of hypertrophic/terminally matured chondrocyte-specific genes. Forskolin treatment also enhanced hyaline cartilage formation by reducing type I collagen gene expression and increasing sulfated glycosaminoglycan accumulation in the developed cartilage. Furthermore, forskolin treatment in vitro increased the frequency at which the cartilage pellets maintained unmineralized chondrocytes after subcutaneous transplantation. To elucidate the type of cartilage that forskolin preferentially promotes and potential molecular mechanisms involved in the forskolin-suppression of chondrocyte hypertrophic differentiation in vitro, we performed genome-wide, comparative transcriptomic analyses on the cartilage pellets formed from 3 to 4 independent pellet cultures of ectomesenchymal cells with or without forskolin treatment. RNAs were isolated on day 26-28 and mRNA-sequencing (RNA-seq) analyses were performed.
2020-06-01 | GSE116173 | GEO
Project description:Transcriptomic signatures of cartilage ageing
| PRJEB1185 | ENA
Project description:We used human fetal bone marrow-derived mesenchymal stromal cells (hfMSCs) differentiating towards chondrocytes as an alternative model for the human growth plate (GP). Our aims were to study gene expression patterns associated with chondrogenic differentiation to assess whether chondrocytes derived from hfMSCs are a suitable model for studying the development and maturation of the GP. hfMSCs efficiently formed hyaline cartilage in a pellet culture in the presence of TGFB3 and BMP6. Microarray and principal component analysis were applied to study gene expression profiles during chondrogenic differentiation. A set of 232 genes was found to correlate with in vitro cartilage formation. Several identified genes are known to be involved in cartilage formation and validate the robustness of the differentiating hfMSC model. KEGG pathway analysis using the 232 genes revealed 9 significant signaling pathways correlated with cartilage formation. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development. To determine the progression of growth plate cartilage formation, we compared the gene expression profile of differentiating hfMSCs with previously established expression profiles of epiphyseal GP cartilage. As differentiation towards chondrocytes proceeds, hfMSCs gradually obtain a gene expression profile resembling epiphyseal GP cartilage. We visualized the differences in gene expression profiles as protein interaction clusters and identified many protein clusters that are activated during the early chondrogenic differentiation of hfMSCs showing the potential of this system to study GP development.
2013-04-22 | GSE40942 | GEO
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