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RNA-Seq analyses in miR-574-5p-transfected mouse splenocytes

ABSTRACT: RNA-Seq analyses in miR-574-5p-transfected mouse splenocytes

PROVIDER: PRJNA990654 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25113851.fastq.gz	Fastqsanger.gz
	SRR25113852.fastq.gz	Fastqsanger.gz
	SRR25113853.fastq.gz	Fastqsanger.gz
	SRR25113854.fastq.gz	Fastqsanger.gz
	SRR25113855.fastq.gz	Fastqsanger.gz

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RNA-Seq analyses in miR-574-5p-transfected mouse splenocytes

Project description:RNA profiling by RNA-Seq analyses showed that in comparison with the control Dotap-treated cells, miR-574-5p transfection for 24 h resulted in significant up-regulation of 277 genes and down-regulation of 80 genes by at least 2-fold in the miR-574-5p-transfected splenocytes. Gene ontology and pathway enrichment analyses showed that the 277 significantly up-regulated genes in miR-574-5p-transfected cells were highly enriched and clustered in pathways associated with interferon and cytokine signaling, antiviral mechanisms, translesion synthesis and autoimmunity .

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Gene expression profiling in miR-574-5p knockdown HeLa cells and the controls

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Project description:Purpose: The target mRNAs of miR-574 in mouse heart are unknown. The goal of this study is to use next generation sequencing (NGS) RNA-seq followed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods to identify the downstream target genes that are directly regulated by miR-574 in murine hearts at the mRNA level. Results: Using a well established data analysis workflow from the Genomic Research Center from University of Rochester Medical Center, we analyzed RNA-seq data. We have identified novel genes that are regulated by miR-574 via miRNA-induced silencing complex (miRISC). We defined differentially regulated genes (either upregulated or downregulated) with statistical significance in total RNA expression change (p value <0.05 for differential expressed genes). We identified 34 upregulated genes involved in the small molecule metabolism and the mitochondrial function, and 49 downregulated genes in the electron transport chain (ETC) complex, oxidative phosphorylation, and tricarboxylic acid cycle. Conclusions: Among 34 upregulated genes, eight genes contain the predicted target seed sequence of miR-574-5p and Fam210a (family with sequence similarity 210 member A) is the only upregulated gene that contains the target seed sequence of both the guide strand miR-574-5p and the passenger strand miR-574-3p. We confirmed that FAM210A was the downstream target of both miR-574-5p and miR-574-3p in vivo and in vitro. Based on our results, we conclude that miR-574 downregulates a limited number of mitochondrial function related genes including FAM210A in mouse hearts at baseline.

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