Project description:Porcine deltacoronavirus (PDCoV) is a newly emerging and special delta coronavirus, which infect mammals such as pigs, cattle and humans, as well as chickens and birds. Exploring RNA structures in the viral genome benefits the understanding of the role of RNA in the lifecycle of viruses. In this study, vRIC-seq is employed to analyze the RNA-RNA interaction in the whole genome structure of PDCoV in virions. About 12.87 and 13.52 million paired reads are obtained in two biological replicates, respectively, with 17.9% and 14.8% of them are identified as valid chimeric reads. These are employed to predict the RNA secondary structure, which is compact and highly structured. A twisted-cyclized conformation is observed in the RNA-RNA interaction map of PDCoV for the first time. 77 multi-way junctions are evenly distributed in the PDCoV genome. Our work provides fundamental structural insights that are essential for understanding the genomic structure and function, genetic evolution, and packaging characteristics of PDCoV.

2024-04-10 | GSE254992 | GEO

The architecture of the Porcine deltacoronavirus RNA genome inside virions by vRICseq

Project description:The architecture of the Porcine deltacoronavirus RNA genome inside virions by vRICseq

| PRJNA1072987 | ENA

Porcine intestinal epithelial cells

Project description:Porcine deltacoronavirus (PDCoV) is an emerging pathogen of swine belonging to family Coronaviridae, genus Deltacoronavirus. PDCoV predominantly infects the porcine intestinal epithelial cells (IPECs) causing severe diarrhea and/or vomiting, dehydration, and death in piglets. However, there are no researches for clarifying the changes of proteins expression levels in the IPECs infected with PDCoV. To better understand the host response to PDCoV infection, in this study, an isobaric tags for relative and absolute quantification (iTRAQ) labeling combined with liquid chromatography-tandem mass spectrometry (LC-MS)-based quantitative proteomic analysis of PDCoV-infected IPEC-J2 cells were performed to investigate the differentially expressed cellular proteins in the PDCoV-infected IPEC-J2 cells. As a result, a total of 5,502 host proteins were quantified at 24 hours post-infection (hpi) in mock and infected cells, among which 78 cellular proteins were differentially expressed with 23 up-regulated proteins and 55 down-regulated proteins. Bioinformatics analysis demonstrated that most of these regulated proteins participated in immune system process and structural molecule activity. Further, expression levels of two representative proteins, ANAPC7 and IFIT1, were confirmed by relative real-time RT-PCR and western blot analysis. The data presented here will provide an overview of host cell response to PDCoV, which could benefit the development of potential antiviral research.

2020-10-19 | PXD019975 | Pride

Project description:Porcine Deltacoronavirus Strains Genome Sequences

| PRJNA1123395 | ENA

MicroRNA expression profile of porcine alveolar macrophages infected with Toxoplasma gondii

Project description:Purpose: Porcine alveolar macrophage was infected by T. gondii including Rh strain and Me49 strain. We want to explore the change of miRNAs after infected with T. gondii in porcine alveolar macrophages. Results: Our study generated six mi RNA expression profiles from macrophages which infect with Rh strain and Me49 and control group in different time. Compare with T. gondii-infected and uninfected with T. gondii, 81 differentially expressed mi RNAs were identified, including 36 novel mi RNAs and 45 mature mi RNAs.

2019-02-07 | GSE119643 | GEO

Porcine rotavirus A

Project description:Complete genome sequence of a porcine rotavirus A strain isolated in france in february 2019

| PRJNA575112 | ENA