RNA-seq of osteogenesis following siRNA depletion of SERPINA3
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE247528 | GEO | 2024/08/05
REPOSITORIES: GEO
Similar Datasets
Project description:SERPINA3 knockdown was observed to reduce cartilage pellet size following differentiation of mesenchymal stem cells (MSCs) to chondrocytes. To understand the global effects on the chondrocyte transcriptome, RNA-sequencing was conducted on primary MSCs depleted of SERPINA3 with siRNA and compared to cells transfected with a siRNA control over a 7 day period.
2024-08-05 | GSE247491 | GEO
Project description:RNA-seq of osteogenesis following siRNA depletion of SERPINA3
| PRJNA1039295 | ENA
Project description:RNA-seq of chondrogenesis following siRNA depletion of SERPINA3
| PRJNA1038778 | ENA
Project description:Bone development and repair depends on the differentiation of mesenchymal stem cells (MSCs) into osteoblasts. MSCs can be differentiated towards osteoblasts in vitro, making these cells a convenient tool for investigation of osteogenesis. Molecular characterization of this process is relevant for the application of MSCs in skeletal regenerative medicine, and for understanding the deregulation of osteogenesis in bone disease. Cellular differentiation is driven by highly regulated changes in gene expression, which at the level of transcription is associated with DNA binding of transcriptional regulators and local changes in chromatin landscape. By sequencing of RNA (RNA-Seq) and immunoprecipitated chromatin (ChIP-Seq) we have characterized gene expression, histone modification changes and DNA binding of the bone master regulator RUNX2 in osteogenic differentiation. Data from the RNA-Seq experiment has also been deposited at ArrayExpress under accession number E-MTAB-1829 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1829/).
2013-09-01 | E-MTAB-1828 | biostudies-arrayexpress
Project description:Bone development and repair depends on the differentiation of mesenchymal stem cells (MSCs) into osteoblasts. MSCs can be differentiated towards osteoblasts in vitro, making these cells a convenient tool for investigation of osteogenesis. Molecular characterization of this process is relevant for the application of MSCs in skeletal regenerative medicine, and for understanding the deregulation of osteogenesis in bone disease. Cellular differentiation is driven by highly regulated changes in gene expression, which at the level of transcription is associated with DNA binding of transcriptional regulators and local changes in chromatin landscape. By sequencing of RNA (RNA-Seq) and immunoprecipitated chromatin (ChIP-Seq) we have characterized gene expression, histone modification changes and DNA binding of the bone master regulator RUNX2 in osteogenic differentiation. Data from the RNA-Seq experiment has also been deposited at ArrayExpress under accession number E-MTAB-1829 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1829/).
2013-09-01 | E-MTAB-1829 | biostudies-arrayexpress
Project description:Objective: Cartilage formation is stimulated in mixtures of chondrocytes and human adipose-derived mesenchymal stem cells (MSCs) both in vitro and in vivo. During co-culture, human MSCs perish through an unknown process. The goal of this study is to elucidate the mechanism by which adipose tissue-derived MSC cell death occurs in the presence of chondrocytes. Methods: Human primary chondrocytes were co-cultured with human MSCs derived from three donors. The cells were cultured in mono-culture or co-culture (20% chondrocytes and 80% MSCs) in pellets (200.000 cell/pellet) for 7 days in chondrocyte proliferation media in hypoxia (2% O2). RNA sequencing was performed to assess for differences in gene expression between monocultures or co-culture. Western blot and immune fluorescence assays were performed to quantify the level of Caspase-3, LC3B and P62. Results: RNA sequencing revealed significant up-regulation of >90 genes in the three co-cultures when compared to monocultures. STRING analysis showed interconnections between >50 of these genes. Remarkably, 75% of these genes play a role in cell death pathways such as apoptosis and autophagy. Western blotting shows a clear up-regulation of the autophagic machinery with no substantial activation of the apoptotic pathway. Conclusion: In co-cultures of human MSCs with primary chondrocytes, MSCs perish through autophagy. We propose that this sacrificial cell death may perhaps contribute to the trophic effects of MSCs on cartilage formation.
2020-06-30 | GSE142831 | GEO
Project description:The recruitment of mesenchymal stem cells in order to reconstruct damaged cartilage of osteoarthritis joints is a challenging tissue engineering task. Vision towards this goal is blurred by a lack of knowledge about the underlying differences between chondrocytes and MSC during the chondrogenic cultivation process. The aim of this study was to shed light on the differences between chondrocytes and MSC occurring during chondral differentiation through tissue engineering. As a model we used the pellet culture system under chondrogenic conditions for the comparison of chondrocyte and MSC differentiation. Immunohistology was followed by microarray analysis, which was filtered through already published datasets describing different developmental processes. Validation was performed with quantitative RT-PCR. Results describe inferior chondrogenic ECM-production by MSCs and underline their closer link to the osteogenic lineage. Chondrocytes have an upregulated fatty acid/cholesterol metabolism which might give hints for future modifications of culture conditions. To shed light on the differences between chondrocytes and MSC occurring during chondral differentiation through tissue engineering, a pellet culture system under chondrogenic conditions for the comparison of chondrocyte and MSC differentiation was used after 0, 3, 7 and 14 days
2010-05-14 | E-GEOD-19664 | biostudies-arrayexpress
Project description:To excavate the genes regulated by SERPINA3, We profiled SERPINA3 silenced differentiated KC versus control using a RNA-seq approach. The genes down regulated in SERPINA3 silenced cells represent targets that are positively regulated by SERPINA3.
2017-07-29 | GSE102000 | GEO
Project description:Purpose:To gain a deeper insight into how Serpina3 regulates neurogenesis and further controling cortex folding in mice brain, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by TCF20 deletion at E15. Methods: Total RNA was extracted from E15 telencephalic tissue of WT and serpina3 cKI mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately approximately one thousand transcripts showed differential expression between the WT and Serpina3 knock-in brain cortex, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the up-regulated genes were enriched in the terms related to neurogenesis, neuronal specification, neural differentiation and secretion by cells. Up-regulated genes showed a significant enrichment of terms involved in up regulation of hypersensitivity and down regulation of inflammatory response. These results reflected the importance of serpina3 in cortical neurogenesis and cortex folding. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how serpina3 contribute to brain cortical development.
2021-01-23 | GSE165345 | GEO
Project description:Declining bone mass is associated with aging and osteoporosis, a disease characterized by progressive weakening of the skeleton and increased fracture incidence. Growth and lifelong homeostasis of bone involve interactions between different cell types including vascular cells and mesenchymal stromal cells (MSCs). As these interactions involve Notch signaling, we have explored whether treatment with secreted Notch ligand proteins can enhance osteogenesis in adult mice. We show that a bone-targeting, high affinity version of the ligand Delta-like 4 (termed Dll4(E12)) induces bone formation without causing adverse effects in other organs, which are known to rely on intact Notch signaling interactions. Single cell analysis of stromal cells indicates that Dll4(E12) primarily acts via bone marrow MSCs and has comparably minor effects on osteoblast lineage cells, endothelial cells or chondrocytes. Based on this example, we propose that bone-targeted fusion proteins might be therapeutically useful and can avoid detrimental effects caused by systemic administration.
2022-01-23 | GSE152285 | GEO