Transcriptomic profiling of mesenchymal stem cells (MSC) differentiation into mesangial cells
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ABSTRACT:
PROVIDER: PRJNA591452 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
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| SRR10528181.fastq.gz | Fastqsanger.gz | |||
| SRR10528182.fastq.gz | Fastqsanger.gz | |||
| SRR10528183.fastq.gz | Fastqsanger.gz | |||
| SRR10528184.fastq.gz | Fastqsanger.gz | |||
| SRR10528185.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: To study the pattern of transcriptomic changes during MSC differentiation into mesangial cells and to identify biomarkers or key genes involved in this differentiation. Methods: Differentiation of MSC into mesangial cells was induced by co-culturing with injured mesangial cells in trans-well dishes (n=3). Total RNA from co-cultured MSC at different time point were extracted before running RNA sequencing. Generated RNA-seq data was analysed. Results and conclusions: A systematic analysis has identified several monotonic pattern key genes (either ascending or descending). These identified descending monotonic key genes are related to stemness or regulation of cell cycle while ascending monotonic key genes are associated with the functions of mesangial cells.
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2016-12-20 | GSE58919 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE20045: A mesoderm-derived mesenchymal stem/stromal cells (MSC) precursor: time course experiment GSE20046: A mesoderm-derived mesenchymal stem/stromal cells (MSC) precursor: stages of development experiment Refer to individual Series
2010-12-03 | E-GEOD-20047 | biostudies-arrayexpress
Project description:Mesenchymal stem/stromal cells (MSCs) are multipotent cells that can differentiate into a variety of cell types forming connective tissue and skeleton, and are essential participants in the development of all organs. However, MSC precursors remain largely unknown. In human embryonic stem cells (hESCs) directed to mesendodermal differentiation through coculture with OP9 stromal cells, we identified a population of mesodermal cells by surface expression of apelin receptor (APLNR1). APLNR+ cells were enriched with precursors generating compact spheroid colonies in semisolid suspension culture. Being formed by single cells, these colonies consisted of a uniform population of mesenchymal cells with a transcriptional profile representative of embryonic mesenchyme originating from lateral plate/extraembryonic mesoderm. Mesenchymal colony formation required serum-free medium and FGF2 as a colony-forming factor, could be significantly enhanced by PDGF-BB, but suppressed by VEGF. When transferred to the adherent cultures in serum-free medium with FGF2, individual colonies gave rise to multipotential mesenchymal cell lines with typical phenotype (CD146+CD105+CD73+CD31-CD43-CD45-), differentiation (chondro-, osteo-, and adipogenesis) and proliferation (>80 doublings) potentials. Consistent with lineage-restricted differentiation pattern, neither endothelial nor hematopoietic cells could be produced from adherent mesenchymal cultures, however endothelial cells could be derived from mesenchymal colonies in the early days of colony-forming culture suggesting that mesenchymal cells arose from cells with primary angiogenic potential (mesangioblasts). Together these studies identified mesangioblasts as the earliest clonogenic mesenchymal precursors at this stage of their specification from mesoderm. This set (11 samples) of expression data is sequential stages of MSC development from hESCs (H1), namely ALPNR+ mesodermal precursors isolated on day 2 and day 3 differentiation, mesangioblast (MB) cores (Day 2 H1-derived cores), hemangioblast (HB) cores (day 3 H1-derived cores), mesangioblast (MB) and hemangioblast (HB) colonies, and colony-derived MSC lines at passage 1 and 5.
2010-12-03 | E-GEOD-20046 | biostudies-arrayexpress
Project description:Adipogenesis is a physiological process required for fat-tissue development, mainly involved in regulating the organism energetic-state. Abnormal distribution-changes and dysfunctions in such tissue are associated to different pathologies. Adipocytes are generated from progenitor cells, via a complex differentiating process not yet well understood. Therefore, we investigated differential mRNA and miRNA expression patterns of human mesenchymal stromal-cells (MSC) induced and not induced to differentiate into adipocytes by next (second)-generation sequencing. A total of 2,866 differentially-expressed genes (101 encoding miRNA) were identified, with 705 (46 encoding miRNA) being upregulated in adipogenesis. They were related to different pathways, including PPARG, lipid, carbohydrate and energy metabolism, redox, membrane-organelle biosynthesis and endocrine system. Downregulated genes were related to extracellular matrix and cell migration, proliferation and differentiation. Analyses of mRNA-miRNA interaction showed that repressed miRNA-encoding genes can act downregulating PPARG-related genes; mostly the PPARG activator (PPARGC1A). Induced miRNA-encoding genes regulate downregulated genes related to TGFB1. These results shed new light to understand adipose-tissue differentiation and physiology, increasing our knowledge about pathologies like obesity, type-2 diabetes and osteoporosis.
2016-08-31 | E-MTAB-4884 | biostudies-arrayexpress
Project description:Background. The in vivo distribution status and molecular signature of bone marrow mesenchymal stem cells (MSC) remain unknown, although ex vivo expanded MSC have been used in numerous studies. Methods/Results. To address these issues, we identified human MSC-characteristic genes, including 9 transcription factor genes - using DNA microarray analysis: Most (75 %) of the MSC-characteristic genes were down-regulated by knockdown of the transcription factors. Furthermore, we used an antibody set for the MSC-characteristic molecules in immunohistochemistry, which revealed that, in embryonic/neonatal mice, elongated MSC were abundant near the endosteum and in the interior of bone marrow, perichondrium and periosteum, whereas in adult mice round/compact MSC were found only in the interior of bone marrow: No MSC-like cells were found in any other skeletal or non-skeletal tissues using this antibody set. Conclusion. The identification of native MSC in developing and adult skeletal tissues should be useful in basic and clinical studies on MSC. Experiment Overall Design: Cell Cultures Experiment Overall Design: Human iliac MSC were purchased from BioWhittaker Inc (Walkersville, MD) or obtained from iliac crest according to protocol approved by ethical authorities at Hiroshima University. Human skin fibroblasts were purchased from KURABO (Osaka, Japan), and human gingival fibroblasts were isolated as described previously (Kawahara K, Shimazu A (2003) Expression and intracellular localization of progesterone receptors in cultured human gingival fibroblasts. J Periodontal Res 38: 242-246.). Culture of MSC and their differentiation from the osteoblast, chondrocyte or adipocyte lineage were performed as described (Matsubara T, Suardita K, Ishii M, Sugiyama M, Igarashi A, et al. (2005) Alveolar bone marrow as a cell source for regenerative medicine: differences between alveolar and iliac bone marrow stromal cells. J Bone Miner Res 20: 399-409.) : We used FGF-2 at 1 ng/mL to expand MSC, because MSC expanded ex vivo with FGF-2 maintained their multidifferentiation potential throughout many mitotic divisions (Tsutsumi S, Shimazu A, Miyazaki K, Pan H, Koike C, et al. (2001) Retention of multilineage differentiation potential of mesenchymal cells during proliferation in response to FGF. Biochem Biophys Res Commun 288: 413-419.). To avoid direct action of FGF-2 on gene expression, FGF-2 was removed from the culture medium of MSC or fibroblasts 72 h before isolation of RNA. Experiment Overall Design: DNA Microarray Analysis Experiment Overall Design: Total RNA was isolated from confluent cultures of 3 lines of MSC (passage 6-9), 3 lines of fibroblasts (passage 7-14), 3 lines of MSC incubated for 28 days in the differentiation-induction medium, using RNeasy Mini Kit (QIAGEN, Chatsworth, CA). DNA microarray analysis was performed by KURABO GeneChip Custom Analysis Service with Human Genome U133 Plus 2.0 chips(Affymetrix. Inc., Santa Clara, CA). The CHP data (Microarray Suite version 5.0, Scaling Factor = 1, Normalization Value = 1, Detection Call a1 = 0.05, a2 = 0.065, Tau = 0.015, Affymetrix Inc.) were standardized by the global median normalization method using GeneSpring (Silicon Genetics, Redwood City, CA). The normalization was limited by flag values, and the median was calculated using the genes that exceeded the Present or Marginal flag restriction. Gene filtering on normalized intensity followed by fold changes (>2-fold) was used to generate the list of genes for expression profiles before or after differentiation.
2008-11-13 | E-GEOD-9451 | biostudies-arrayexpress
Project description:Mesenchymal stem cells (MSC) resemble a multipotent adult stem cell population capable of differentiation into a number of different mesodermal cell types including adipodytes, osteoblasts, chondroblasts. Although still in debate there is some evidence, that these cells can also differentiate into cells of non-mesodermal germal layers including hepatocytes, myocytes, cardiomyocytes or neurons. Analysis of these cells in the course of differentiation makes them an intriguing model for the examination of stemness. More importantly the differentiation capacity of MSC raises high hopes for clinical applications. In this study we have isolated MSC from bone marrow under two different culture conditions, from adipose tissue and from umbilical cord blood. The genome wide gene expression profile of these different human MSC was compared with reference RNA of non-multipotent human fibroblasts HS68. The aim of this study was to elucidate common molecular characteristics of MSC as well as differences in their expression profile. These results might help for a better understanding of MSC and contribute to a reliable quality control that will be necessary for clinical applications.
2005-08-23 | E-EMBL-4 | biostudies-arrayexpress
Project description:To analyze the changes induced in MSC transcriptome by activated T cells, MSC were co-cultured in transwell with anti CD3/CD28 activated T cells for 48 hrs before RNA extraction IFNγ-induced plasticity of mesenchymal stem cells is regulated by STATs through inhibition of mTOR and TGFβ pathways. Vigo T, Procaccini C, Ferrara G, Baranzini S, Oksenberg J, Diaspro A, Kerlero de Rosbo N, Uccella A. The expression of MSC co-cultured with activated T cells ( two replicates) were compared to that of naive MSC (3 replicates)
2015-12-08 | E-GEOD-75749 | biostudies-arrayexpress