MiRNA expresion data from human induced pluripotent stem cells
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ABSTRACT:
PROVIDER: PRJNA483052 | ENA |
REPOSITORIES: ENA
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Project description:We used miRNA array to detail the global miRNA expression of human induced pluripotent stem cells
2019-03-28 | GSE117739 | GEO
Project description:To gain insight into the molecular regulation of human heart development, a detailed comparison of the mRNA and miRNA transcriptomes across differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes and biopsies from fetal, adult, and hypertensive human hearts was performed. Gene ontology analysis of the mRNA expression levels of the hiPSCs differentiating into cardiomyocytes revealed 3 distinct groups of genes: pluripotent specific, transitional cardiac specification, and mature cardiomyocyte specific. Hierarchical clustering of the mRNA data revealed that the transcriptome of hiPSC cardiomyocytes largely stabilizes 20 days after initiation of differentiation. Nevertheless, analysis of cells continuously cultured for 120 days indicated that the cardiomyocytes continued to mature toward a more adult-like gene expression pattern. Analysis of cardiomyocyte-specific miRNAs (miR-1, miR-133a/b, and miR-208a/b) revealed a miRNA pattern indicative of stem cell to cardiomyocyte specification. A biostatistitical approach integrated the miRNA and mRNA expression profiles revealing a cardiomyocyte differentiation miRNA network and identified putative mRNAs targeted by multiple miRNAs. Together, these data reveal the miRNA network in human heart development and support the notion that overlapping miRNA networks re-enforce transcriptional control during developmental specification. miRNA expression profiling of differentiating human-induced pluripotent stem cell (hiPSC)–derived cardiomyocytes (days 0-120)
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Project description:Chemical warfare nerve agents (CWNA) are potent cholinesterase inhibitors that may also have non-cholinesterase effects. Several in vivo studies have shown that exposure to CWNA compounds induces damage in the brain and heart. Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures. This study utilized microRNA (miRNA) analysis to evaluate potential direct cellular effects of the nerve agent VX (o-ethyl-s-[2 (diisopropylamino) ethyl] methylphosphonothiolate) on human-induced pluripotent stem cell (iPSC)-derived neurons iPSC-derived neurons were treated with VX at concentrations of 0µM (saline control), 0.1µM or 100µM for either 1 hour or 6 hours. Total RNA was then isolated and processed for miRNA microarray analysis using Affymetrix miRNA 2.0 GeneChips
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Project description:Chemical warfare nerve agents (CWNA) are potent cholinesterase inhibitors that may also have non-cholinesterase effects. Several in vivo studies have shown that exposure to CWNA compounds induces damage in the brain and heart. Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures. This study utilized microRNA (miRNA) analysis to evaluate potential direct cellular effects of the nerve agent GD/soman (O-Pinacolyl methylphosphonofluoridate) on human-induced pluripotent stem cell (iPSC)-derived neurons iPSC-derived neurons were treated with GD at concentrations of 0µM (saline control), 0.1µM or 100µM for either 1 hour or 6 hours. Total RNA was then isolated and processed for miRNA microarray analysis using Affymetrix miRNA 2.0 GeneChips
| E-GEOD-48669 | BioStudies
Project description:Chemical warfare nerve agents (CWNA) are potent cholinesterase inhibitors that may also have non-cholinesterase effects. Several in vivo studies have shown that exposure to CWNA compounds induces damage in the brain and heart. Underlying mechanisms of this damage are a critical area of research for the development of medical countermeasures. This study utilized microRNA (miRNA) analysis to evaluate potential direct cellular effects of the nerve agent GD/soman (O-Pinacolyl methylphosphonofluoridate) on human-induced pluripotent stem cell (iPSC)-derived cardiomyocytes iPSC-derived cardiomyocytes were treated with GD at concentrations of 0µM (saline control), 0.1µM or 100µM for either 1 hour or 6 hours. Total RNA was then isolated and processed for miRNA microarray analysis using Affymetrix miRNA 2.0 GeneChips
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Project description:Introduction:Pluripotent stem cells are believed to have greater clinical potential than mesenchymal stem cells due to their ability to differentiate into almost any cell type of an organism, and since 2006, the generation of patient-specific induced pluripotent stem cells (iPSCs) has become possible in multiple species. Objectives:We hypothesize that different cell types respond differently to the reprogramming process; thus, the goals of this study were to isolate and characterize equine adult and fetal cells and induce these cells to pluripotency for future regenerative and translational purposes. Methods:Adult equine fibroblasts (eFibros) and mesenchymal cells derived from the bone marrow (eBMmsc), adipose tissue (eADmsc), and umbilical cord tissue (eUCmsc) were isolated, their multipotency was characterized, and the cells were induced in vitro into pluripotency (eiPSCs). eiPSCs were generated through a lentiviral system using the factors OCT4, SOX2, c-MYC, and KLF4. The morphology and in vitro pluripotency maintenance potential (alkaline phosphatase detection, embryoid body formation, in vitro spontaneous differentiation, and expression of pluripotency markers) of the eiPSCs were characterized. Additionally, a miRNA profile analysis of the mesenchymal and eiPSCs was performed. Results:Multipotent cells were successfully isolated, but the eBMmsc failed to generate eiPSCs. The eADmsc-, eUCmsc-, and eFibros-derived iPSCs were positive for alkaline phosphatase, OCT4 and NANOG, were exclusively dependent on bFGF, and formed embryoid bodies. The miRNA profile revealed a segregated pattern between the eiPSCs and multipotent controls: the levels of miR-302/367 and the miR-92 family were increased in the eiPSCs, while the levels of miR-23, miR-27, and miR-30, as well as the let-7 family were increased in the nonpluripotent cells. Conclusions:We were able to generate bFGF-dependent iPSCs from eADmsc, eUCmsc, and eFibros with human OSKM, and the miRNA profile revealed that clonal lines may respond differently to the reprogramming process.
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Project description:MicroRNAs (miRNAs) are a newly discovered endogenous class of small noncoding RNAs that play important posttranscriptional regulatory roles by targeting mRNAs for cleavage or translational repression. Accumulating evidence now supports the importance of miRNAs for human embryonic stem cell (hESC) self-renewal, pluripotency, and differentiation. However, with respect to induced pluripotent stem cells (iPSC), in which embryonic-like cells are reprogrammed from adult cells using defined factors, the role of miRNAs during reprogramming has not been well-characterized. Determining the miRNAs that are associated with reprogramming should yield significant insight into the specific miRNA expression patterns that are required for pluripotency. To address this lack of knowledge, we use miRNA microarrays to compare the "microRNA-omes" of human iPSCs, hESCs, and fetal fibroblasts. We confirm the presence of a signature group of miRNAs that is up-regulated in both iPSCs and hESCs, such as the miR-302 and 17-92 clusters. We also highlight differences between the two pluripotent cell types, as in expression of the miR-371/372/373 cluster. In addition to histone modifications, promoter methylation, transcription factors, and other regulatory control elements, we believe these miRNA signatures of pluripotent cells likely represent another layer of regulatory control over cell fate decisions, and should prove important for the cellular reprogramming field.
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Project description:The wide application of pig disease model has caused a surge of interest in the study of derivation of pig induced pluripotent cells (iPSCs). Here we performed genome-wide analysis of gene expression profiling by RNA-seq and small RNA-seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and microRNA transcripts that were specifically expressed in pig iPSCs. Our analysis identifies the genes up-regulated in pig iPS compared with somatic cells and also the differentially expressed genes between pig iPSCs under different culture medium. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to “ribosome”, “chromatin remodeling”, and genes involved in “cell cycle “that may be critical to maintain their pluripotency, plasticity, and stem cell function. Our analysis demonstrates the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. Specifically, the data indicate distinctive expression patterns for SALL4 spliced variants in different pig cell types and highlight the necessity of defining the type of SALL4 when addressing the expression of this gene in pig cells. MeDIP-seq data revealed that the distribution patterns of methylation signals in pig iPS and somatic cells along the genome. We identify 25 novel porcine miRNA, including pluripotency-related miR-302/367cluster up-regulated in pig iPSCs. At last, we profile the dynamic gene expression signature of pluripotent genes in the preimplantation development embryo of pig. The resulting comprehensive data allowed us to compare various different subsets of pig pluripotent cell. This information provided by our analysis will ultimately advance the efforts at generating stable naïve pluripotency in pig cells.
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Project description:Embryonic stem cells are pluripotent and possess the ability to differentiate into numerous lineages during the developmental process. In similarity to embryonic stem cells, human induced pluripotent stem cells (iPSCs) possess the potential to differentiate into multiple lineages making them an excellent research tool. We generated iPSCs from multiple donors and also differentiated iPSCs from these donors into human neural progenitor cells (NPCs). We used human transcriptome arrays to detail the programme of gene expression underlying NPC induction and identified distinct classes of up-regulated genes during this process. Total RNAs were extracted from human induced pluripotent stem cells and induced pluripotent stem cell-derived neural progenitor cells. Their gene expression profiles were investigated using the Affymetrix GeneChip Human Transcriptome Array 2.0 platform.
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Project description:Expression data from undifferentiated human induced pluripotent stem cells total RNA was isolated from undifferentiated induced pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.
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