Ontology highlight
ABSTRACT:
PROVIDER: PRJNA797671 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17631821_1.fastq.gz | Fastqsanger.gz | |||
| SRR17631821_2.fastq.gz | Fastqsanger.gz | |||
| SRR17631822_1.fastq.gz | Fastqsanger.gz | |||
| SRR17631822_2.fastq.gz | Fastqsanger.gz | |||
| SRR17631823_1.fastq.gz | Fastqsanger.gz |
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Project description:To investigate the changes in circRNAs expression after SVA infection in PK-15 cells, we established a model of SVA-infected PK-15 cells.
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Project description:Senecavirus A (SVA) belongs to the family of small RNA viruses, the genus Senecavirus, and has become a research hotspot because of the oncolytic viral characteristics. PIWI-interacting RNAs (piRNAs) are a class of small RNAs found in mammalian cells in recent years; however, the host piRNA expression profile during SVA infection and their role in viral infection is not well understood. In this study, we obtained small RNA transcriptome expression profiles from SVA-infected pig kidney cell lines (PK-15) by high-throughput sequencing. Differential expression (DE) analysis, GO annotation, and KEGG analysis of piRNAs in SVA-infected and non-infected PK-15 cells were performed. qRT-PCR was used to validate the DE of piRNAs. The results showed that 981 and 1,370 novel piRNAs were identified in SVA-infected and non-infected PK-15 cells; expression of 129 piRNAs was upregulated while that of 44 piRNAs was downregulated after SVA infection. The DE of 10 piRNAs was further verified by qRT-PCR. GO annotation analysis results showed the metabolism, proliferation, and differentiation were significantly activated after SVA infection. KEGG results showed that after SVA infection, piRNA was mainly enriched in AMPK signaling pathway, Rap1 signaling pathway, circadian rhythm, and VEGF signaling pathway, which suggested that piRNAs may play a role in regulating antiviral immunity, intracellular homeostasis, and tumor processes during SVA infection. This is the first report of the piRNA transcriptome in pig kidney cells and will contribute to the research of piRNA regulatory mechanism during SVA infections and provide an important reference for the prevention and treatment of SVA.
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Project description:Effect of SVA infection on circRNAs expression in PK-15 cells
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Project description:Purpose: to study the changes in various genes in cells during the early stages of SVA infection. Differentially expressed genes were screened from them, and GO enrichment analysis and KEGG pathway enrichment analysis were performed. This study provides some help for better prevention and control of SVA infection. Methods: Deep sequencing of SVA-infected cells at 6hpi and 12hpi and mock-infected cells were performed, in triplicate. The raw data from the sequencing is filtered using ngqc software and compared to the reference sequence. Differential and enrichment analyses were then performed. PK:mock-infeted groups TP:SVA-infected groups Results: Using RNA-seq technology, more than 46 billion raw reads of each sample were generated, and the proportion of clean reads was >94%. The ratios of clean reads successfully mapped to the swine reference genome in all samples ranged from 90.41% to 95.92%, and the ratios of the uniquely mapped reads were >91.48%. The R2 values of the samples in the same group were >0.99. 1584 genes had a significant difference at 6hpi between SVA- and mock-infected groups and 9785 DEGs were screened at 12hpi, 28 of these DEGs were validated with RT–qPCR. Altered expression of 28 genes was confirmed with RT–qPCR, demonstrating the high degree of sensitivity of the RNA-seq method. At the same time, we selected three important DEGs for WB experiments and analyzed their protein-level alterations. The results were consistent with RNA-seq data, Further confirmation of the accuracy of RNA-SEQ technology Conclusion: Our experiments analyzed in detail the changes in various genes in cells after SVA infection. A series of cytokines, such as interleukins (IL6, TNF-α), chemokines (CCL4, CCL5), and immune-related factors (IFN-α, IFN-β, RSAD2, MX1), are involved in the battle between SVA and the host. We postulated that this innate immune response is the main mean used by the host for the initial response to SVA infection. This study evaluated SVA-induced immune responses and provides information that can be used to investigate the molecular mechanisms of SVA-host interactions.
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Project description:Seneca Valley Virus (SVV) or commonly known as Senecavirus A (SVA), is one of picornavirus that is associated with vesicular disease and neonatal mortality in swine herds. However, the pathogenesis of SVV remains largely elusive. Our previous study found that SVV replicates extremely faster in porcine IBRS-2 cells than that in porcine PK-15 cells. However, the underlying mechanism remains unknown. In this study, we comprehensively compared the expression features between IBRS-2 cells and PK-15 cells in response to SVV infection by an unbiased high-throughput quantitative proteomic analysis. We found that the innate immune response-realted pathways were efficiently activated in PK-15 cells but not in IBRS-2 cells during SVV infection. A large amount of interferon-stimulated genes (ISGs) were induced in PK-15 cells. In contrast, no ISGs were induced in IBRS-2 cells after SVV infection. This different expression features in the two cell lines was verified by qPCR analysis. Besides, we determined similar results in the two cell lines during another porcine picornavirus foot-and-mouth disease virus (FMDV) infection. Further study demonstrated that the Janus kinase signal transducer and activator of transcription (JAK-STAT) signaling pathway was functioning properly in both IBRS-2 and PK-15 cells. A systematic screening study revealed that the aberrant signal transduction from TBK1 to IRF3 in the RIG-I-like receptor signaling pathway in IBRS-2 cells was the fundamental cause of the different innate immune response manifestation and different viral replication rate in the two cell lines. Together, our findings determined the different feature of IBRS-2 and PK-15 cell lines which will provide useful guidance for choosing right cell line in porcine picornaviruses-mediated host immune signaling research and could be easily extended to other porcine viruses.
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