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ABSTRACT:
PROVIDER: PRJNA1109448 | ENA |
REPOSITORIES: ENA
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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.
2023-01-05 | GSE222010 | GEO
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.
2020-05-12 | GSE150242 | GEO
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.
2023-05-18 | GSE231770 | GEO
Project description:Purpose: Evaluation of the m6A modification of PRV and PK15 transcripts during PRV infection Methods: Porcine kidney cell line PK15 was uninfected or infected with PRV for 24 hours. Total RNA from each sample were extracted. Intact mRNA was isolated from total RNA samples and then chemically fragmented to 300-nucleoside-long fragments. Fragmented mRNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody (a part of the fragmented mRNAs was kept as input). Both m6A enriched mRNAs and input mRNAs were concentrated for RNA-seq libraries construction. The libraries were forwarded to sequencing run on Illumina NovaSeq 6000. Results: PRV transcripts were m6A modified during PRV infection and PRV infection changed m6A modification profiles of PK15 transcripts.
2022-11-02 | GSE209949 | GEO
Project description:Senecavirus A (SVA) belongs to the genus Senecavirus in the family Picornaviridae. It is increasingly used for proteomic research that tandem mass tag-labeled liquid chromatography-tandem mass spectrometry is combined with the parallel reaction monitoring technique. In this study, this combined method was used to uncover separately proteomic profiles of SVA- and non-infected BSR-T7/5 cells. Further, both proteomic profiles were compared with each other. The proteomic profiling showed that a total of 361 differentially expressed proteins were identified, out of which, 305 and 56 were upregulated and downregulated in SVA-infected cells at 12 h post-inoculation, respectively. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses showed that cellular metabolisms were mainly affected in SVA-inoculated cells at an early stage of infection.
2021-09-10 | PXD024947 | Pride
Project description:Senecavirus A (SVA), which is associated with swine vesicular disease, is an emerging pathogen that caused considerable damages to Chinese pig industrial. As a powerful research method, proteomic provides clues for diseases diagnose, medicine targets selection and pathogenic immunity researches. By using of proteomic to study PK-15 cells infected with SVA SDta/2018 strain, this research aimed to obtain insights and clues for investigating pathogenesis of SVA, viral immune escape mechanism and viruses induced impacts to host immune response.
2022-06-09 | PXD031260 | Pride
Project description:We employed deep sequencing technology to uncover cellular miRNAs differentially regulated after expression of each of three PCV2-encoded open reading frames (ORFs) in porcine kidney epithelial PK15 cells. Control PK15 vs. PCV2 ORF1, ORF2, ORF3-expressing PK15.
2014-08-08 | E-GEOD-60206 | biostudies-arrayexpress
Project description:X-linked dystonia parkinsonism (XDP) is an inherited neurodegenerative disease characterized by the antisense insertion of an SVA retrotransposon into the TAF1 gene, encoding for the largest subunit of the basal transcription factor TFIID, which is essential for RNA polymerase II activity. This SVA insertion has been associated with altered TAF1 expression levels, but the cause of this outcome and its link to the development of XDP remain unknown. Unique to the XDP SVA compared to other SVA retrotransposons in the human genome is the amplification of the (GGGAGA)n repeat domain, creating a unique G4-prone region, whose length correlates with age at onset and disease severity. By ChIP-seq and ChIP-qPCR with the anti-G4 antibody BG4, we assessed that G4s are present in the folded state in the XDP SVA of these cells. Using available G4 ligands, we demonstrated that stabilization of the XDP SVA G4s reduces TAF1 transcripts in the exons around and downstream of the SVA, while increasing the transcription of the upstream exons, possibly through a positive feedback loop.
2024-09-04 | GSE250293 | GEO