Comparison of the transcriptome across cardiac cell types and cellular compartments
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ABSTRACT:
PROVIDER: PRJNA675480 | ENA |
REPOSITORIES: ENA
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Project description:Background and Objective: Currently, the cells for transplantation were derived from either autologous or allogeneic tissue. The former has a drawback that the quality of donor cells could depend on the patient’s condition, and the quantity could also be limited. To solve these problems, we investigated the potential of allogeneic cardiac mesenchymal progenitors (CMPs) derived from postmortem heart, which might be an immunological privileged like bone marrow-derived mesenchymal progenitors. Materials and Methods: We examined whether viable CMPs could be isolated from murine postmortem cardiac tissue that was harvested 24 hours postmortem. After two to three weeks propagation with high dose of basic fibroblast growth factor, we performed the cellular characteristics analyses, which included proliferation and differentiation property flow cytometric analyses, and microarray analyses. Results: Postmortem CMPs had longer lag phase after seeding than CMPs from living tissues, but they demonstrated the similar characteristics in all above examinations. In addition, global gene expression analysis by microarray indicated the similar characteristics between the cell derived from postmortem and living tissue. Conclusion: These results indicate allogeneic postmortem CMPs could have promising potential for cell transplantation as clinical applications, because of circumventing the issue of brain death. The samples were collected fom living or postmortem cardiac tissue (24 hr at 4C). We generated cardiac mesenchymal progenitors (CMPs) from these cardiac tissue, and compared global gene expression by AgilentMouse GE 8x60k Microarray. Adult, or fetal mouse heart RNAs were used as positive control. Adult mouse total heart RNAs were purchased from Clontech. Fetal mouse heart was extracted from fetus which is embryonic day 16.5 C57BL/6 strain. Tg means Transgenic mouse (C57BL/6-Tg(Myh6-EGFP)MG2).
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Project description:Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)–Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The ‘omic’ results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)–seq data were obtained to provide new insights into PSV-P–satRNA–plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.
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