AMPK related of circRNA expression in C57 male mice myocardium
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ABSTRACT:
PROVIDER: PRJNA1167178 | ENA |
REPOSITORIES: ENA
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Project description:To identify adenosine monophosphate-activated protein kinase (AMPK)-related circular RNA (circRNA) that was differentially expressed in the mouse myocardial ischaemia-reperfusion injury (MIRI) model, and map the AMPK-related circRNA network to provide novel insights for the prevention and treatment of MIRI.
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Project description:To build a circRNA-miRNA-mRNA network in the condition of NPRA deletion in the heart, we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs in NPRA-/- and NPRA+/+ myocardium tissues.
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Project description:circRNA expression in NPRA-/- and NPRA+/+ myocardium tissues
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Project description:Arraystar Human circRNA Microarray is designed for the global profiling of human circRNAs. In this study, we applied a circRNA microarray to screen the potential biomarker for HCC. 20 samples extracted from plasma samples including HCC group before operation, and after operation, CH group and control group. Each group contained five samples.
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Project description:Many studies have demonstrated the importance of circRNA in regulating gene expression through functioning as microRNA sponges. However, the roles of circRNA-protein interaction are not fully understood. Importantly, how circRNA-protein interaction contributes the progression of pancreatic ductal adenocarcinoma is largely unexplored. Therefore, RNA Pull down assay for investigating RNA-protein interaction was performed in PANC-1 cells.
2022-02-15 | PXD015048 | Pride
Project description:Purpose: The goals of this study are to compare adult male and female C57 mouse hearts transcriptome profiling (RNA-seq) to conclude cardiac sex differences at the mRNA level. Methods: mRNA profiles of adult male and female C57 mouse hearts were generated by deep sequencing, n=4 for each sex, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 50 million sequence reads per sample to the mouse genome (build mm10) and identified 16,160 transcripts in the mouse hearts.
2021-08-25 | GSE182691 | GEO
Project description:Purpose: The goals of this study are to compare E9.5 male and female C57 mouse embryonic hearts transcriptome profiling (RNA-seq) to conclude cardiac sex differences at the mRNA level. Methods: mRNA profiles of E9.5 male and female C57 mouse embryonic hearts were generated by deep sequencing, n=4 for each sex, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) and identified 16,460 transcripts in the mouse hearts.
2021-08-25 | GSE182690 | GEO
Project description:To investigate the difference of gene expression between kidneys of groups with different treatments, We performed gene expression profiling analysis using data obtained from RNA-seq of kidney from socially stressed male C57 BL/6 mice with different treatments.
2023-09-15 | GSE207710 | GEO
Project description:AMP-activated protein kinase (AMPK) is a major regulator of cellular energy homeostasis that coordinates metabolic pathways in order to balance nutrient supply with energy demand. AMPK elicits acute and diverse metabolic effects by directly phosphorylating various targets. AMPK activation also promotes metabolic reprogramming in longer term via effects on gene expression. The aim of this study is to elucidate molecular mechanism(s) by which AMPK activation modulates metabolic adaptation through its impact on gene regulation.
2019-03-04 | GSE104170 | GEO
Project description:Circular RNAs (circRNAs), a noncoding RNA class originating from alternative splicing, are highly abundant in neural tissues and were shown to regulate gene expression e.g. by interacting with microRNAs and RNA-binding proteins. Neuroblastoma is an embryonal neoplasia, which arises from undifferentiated neural crest cells. Here, we aimed to explore, whether circRNAs influence the pathogenesis of high-risk neuroblastoma. We performed whole-transcriptome sequencing of 104 primary neuroblastoma samples of all risk-groups and identified 5,203 unique circRNAs involving 2,302 genes. Candidate circRNA expression did not correlate with host gene expression, indicating independent regulatory mechanisms. circRNAs were significantly downregulated in the MYCN-amplified high-risk tumors. These findings were independently reproduced in a tetracycline-inducible MYCN-overexpression system based on a non MYCN-amplified neuroblastoma cell line, suggesting that MYCN drives this global circRNA repression. We identified the RNA helicase DHX9 as a mediator of this global suppressive effect of MYCN on circRNAs. Comparing our RNA sequencing data with other cancers and controls revealed a circRNA subset specifically upregulated in neuroblastoma that included a circRNA derived from the ARID1A tumor suppressor gene. Specific circARID1A knockdown resulted in reduced proliferation, cell numbers and viability, prompted apoptosis and induced a differentiated phenotype. Neither knockdown, nor overexpression of circARID1A influenced ARID1A mRNA and protein levels significantly. To dissect the potential mode of function, we performed a pulldown assay with subsequent mass spectrometry. We identified the RNA-binding protein KHSRP as an interaction partner that participates in the mechanism of action of circARID1A. In summary, this study highlights an important role of circRNAs in neuroblastoma biology and may establish this RNA class as a future therapeutic target and biomarker.
2023-04-06 | PXD026053 | Pride