Similar Datasets
Project description:Transcriptomics of BMSCs and BMDMs
| PRJNA1192299 | ENA
Project description:The BMSCs were cultured with unirradaited/irradiated DC-CM for 3 days. Total RNA was extracted and sent to DIATRE biological technology company (China) for library preparation, RNA-seq, and data analysis. DESeq2 package was carried out to perform differential expression analysis, and differentially expressed genes (DEGs) were determined by a P value <0.05. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis were utilized to detect the molecular and biological processes as well as signaling pathways.
2025-06-30 | GSE292155 | GEO
Project description:To investigate the gene expression changes after Grx2 knockout, we isolated primary BMSCs from Grx2+/+ and Grx2-/- mice and passaged them to the 7th generation. Then, we performed gene expression analysis using RNA-seq data from six cell samples (three replicates per group).
2025-04-11 | GSE293959 | GEO
Project description:To investigate the gene expression profile of macrophages in response to Salmonella infection in vitro, we differentiated mouse BMDMs and the cells were used as a model for Salmonella infection We then performed gene expression profiling analysis using data obtained from RNA-seq of BMDMs at two conditions (uninfected and Salmonella-infected cells).
2024-07-31 | GSE239543 | GEO
Project description:Bone marrow and BMDMs (unstimulated) RNA-seq
| PRJNA632847 | ENA
Project description:Osteoradionecrosis of the jaw (ORNJ) is a complication after head and neck radiotherapy that severely affects patients’ quality of life. Currently, an overall understanding of microenvironmental factors of ORNJ is still lacking. Here, we reveal the activation of taurine metabolism in irradiated mandibular stromal cells with scRNA-Seq and the decrease of taurine in irradiated bone marrow mesenchymal stromal cells (BMSCs) with metabolomics. Compared to the unirradiated BMSCs, the taurine uptake of irradiated BMSCs increases. The taurine concentration in peripheral blood and jaws of irradiated mice are significantly lower than the unirradiated mice. Supplementation of taurine promotes osteogenic differentiation, decreases oxidative stress and DNA damage of irradiated BMSCs. Oral administration of taurine significantly promotes survival rate of irradiated mice and promotes osteogenesis of irradiated jaws. Our study sheds light on the role of taurine during the recovery of radiation-induced jaw injury, suggesting a potential non-invasive therapeutic means to combat ORNJ.
2024-07-08 | MTBLS10284 | MetaboLights
Project description:Abstract Background: Bone marrow stromal cells (BMSCs) are being used for immune modulatory, anti-inflammatory and tissue engineering applications, but the properties responsible for these effects are not completely understood. Human BMSCs were characterized to identify factors that might be responsible for their clinical effects and biomarkers for assessing their quality. Methods: Early passage BMSCs prepared from marrow aspirates of 4 healthy subjects were compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. The cells were analyzed with oligonucleotide expression microarrays with more than 35,000 probes. Results: BMSC gene expression signatures of BMSCs differed from those of hematopoietic stem cells (HSCs), hESCs and fibroblasts. Genes up-regulated in BMSCs were involved with cell movement, cell-to-cell signaling and interaction and proliferation. The BMSC up-regulated genes were most likely to belong to integrin signaling, integrin linked kinase (ILK) signaling, NFR2-mediated oxidative stress response, regulation of actin-based motility by Rho, actin cytoskeletal signaling, caveolar-mediated endocytosis, clathrin-mediated endocytosis and Wnt/beta catenin signaling pathways. Among the most highly up-regulated genes were structural extracellular (ECM) proteins: alpha1 and beta1 integrin chains, fibronectin, collagen type IIIalpha1, and collagen type Valpha1 and functional EMC proteins: connective tissue growth factor (CTGF) and transforming growth factor beta induced protein (TGFBI) and ADAM12. Conclusions: Global analysis of human BMSCs suggests that they are mobile, metabolically active, proliferative and interactive cells that make use of integrins and integrin signaling. They produce abundant ECM proteins; some of which may contribute to their clinical immune modulatory and anti-inflammatory effects. Seven samples from early passage BMSCs were prepared from marrow aspirates of healthy subjects and compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. Total RNA from a pool of PBMCs from six healthy subjects was extracted and amplified into aRNA to serve as a reference.
2011-09-20 | E-GEOD-24871 | biostudies-arrayexpress
Project description:Bone marrow mesenchymal stem cells (BMSCs) differentiate into various mature cell types, including adipocytes and osteoblasts, which is determined by genetic, molecular mediators and local microenvironment. With age, BMSCs become inclined to undergo differentiation into adipocytes rather than osteoblasts, resulting in an increased number of adipocytes and a decreased number of osteoblasts, causing osteoporosis. The dysregulated the gene expression in BMSCs during aging were analyzed. We used microarrays to detail the global programme of gene expression duing aing in BMSCs.
2018-08-15 | GSE116925 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived IL4/IL13 treated BMDMs transcriptome profiling (RNA-seq) to quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods. Methods: BMDMs mRNA profiles of 8 weeks old wild-type (WT) mice were generated, stimulated with IL4/IL13, IL4/IL13+ TNF or TNF, deep sequenced, in triplicate, using Illumina NovaSeq 6000 platform. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9). Conclusions: Our study represents the first detailed analysis of IL4/IL13 or IL4/IL13+TNF stimulated BMDMs, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2021-05-04 | GSE169348 | GEO
Project description:Expression data from young and aged BMSCs
| PRJNA480646 | ENA