Ontology highlight
ABSTRACT:
PROVIDER: PRJNA513899 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8421360.fastq.gz | Fastqsanger.gz | |||
| SRR8421351.fastq.gz | Fastqsanger.gz | |||
| SRR8421361.fastq.gz | Fastqsanger.gz | |||
| SRR8421352.fastq.gz | Fastqsanger.gz | |||
| SRR8421362.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptome sequencing of IPEC-J2 cells infected with PEDV
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Project description:Swine coronavirus-porcine epidemic diarrhea virus (PEDV) with specific susceptibility to pigs has existed for decades, and recurrent epidemics caused by mutant strains have swept the world again since 2010. Here, single-cell RNA-sequencing was used to perform a systematic analysis of pig small intestines infected with PEDV for the first time. Multiple cell types were identified by representative markers, including the unique marker DNAH11 of tuft cells. Meanwhile, the goblet and tuft cells were also susceptible to PEDV except enterocytes. PEDV infection obviously upregulated REG3G, which significantly inhibited virus replication. Notably, IFN-DELTAs in goblet and enterocyte progenitor cells were increased in virus infected piglet, and IFN-DELTA5 could induce GBP1, ISG15, OAS2 and IFITM1 dramatically raised in IPEC-J2 cells and restricted PEDV replication. Complement molecules were mainly expressed in intestinal cells excepting tuft cells, but PEDV decreased C3, C4A, and C5 in enterocytes, thus escaping the antiviral effect of C3. Finally, enterocytes expressed almost all coronavirus entry factors, and PEDV infection caused significant upregulation of the coronavirus receptor ACE2 in porcine enterocyte cells. In summary, this study systematically studied the response of different cell types in small intestine of pigs after PEDV infection, which deepened the understanding of viral pathogenesis.
2022-04-27 | GSE175411 | GEO
Project description:Deoxynivalenol (DON) frequently detected in a wide range of foods and feeds, inducing cytotoxicity to animals and humans. N6-methyladenosine (m6A) is an important epitranscriptomic marker with high abundance in eukaryotic mammals mRNAs. However, the role of the m6A methylomes in DON damage is still poorly understood. Here, we investigated the m6A transcriptome-wide profile in intestinal porcine epithelial cells (IPEC-J2) with and without 1000 ng/mL DON treatment via m6A sequencing and RNA sequencing. In total, 5406 new m6A peaks appeared with the disappearance of 2615 peaks in DON-induced IPEC-J2. The unique m6A-modified genes in DON-induced IPEC-J2 were associated with TNF signaling pathway. We identified 733 differentially expressed mRNA transcripts with hyper-methylated or hypo-methylated m6A peaks between DON-induced IPEC-J2 and normal IPEC-J2. Protein interaction network analysis and qPCR validation suggested that CSF2 probably acts as a promising new target for combating DON damage in IPEC-J2. Our first report of m6A transcriptome-wide map of IPEC-J2 cells presented here provides a starting roadmap for uncovering m6A functions that may affect DON infection.
2020-08-13 | GSE156078 | GEO
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.
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Project description:The intestinal epithelial cell lines 1 and J2 (IPEC-1, IPEC-J2) - spontaneously immortalised cell lines from the porcine intestine - are important tools for studying intestinal function. Microarrays (GeneChip Porcine Genome Array) were used to compare the expression pattern at basal in vitro conditions. Expression analyses complemented by morphological, functional and biochemical analyses revealed that IPEC-J2 is a morphologically and functionally more differentiated cell line in comparison to IPEC-1. In addition, IPEC-2 cells are a preferential tool for in vitro studies with the focus on metabolism.
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Project description:PEDV infection in IPEC-J2 cells caused the change of circRNA expression pattern
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Project description:The immune system is thought to be fragile in the neonate, which is susceptible to pathogens. Exosomes are a type of vehicles existing in the body fluid and participate in many biological processes, especially the immune response. Inorder to investigate the roles that exosomes may play during virus infection in the neonate, porcine epidemic diarrhea virus (PEDV), a devastating enteric virus to newborn piglets, was selected for infection. Serum exosomes were then isolated from the newborn-piglets infected or mock-infected with PEDV and followed by a label-free LC-MS/MS based comparative quantitative proteomic analysis. Among 441 proteins detected in the serum exosomes, there were lots of complement proteins. The expression level of the complement C3, C6 and CFB suffered drastic changes due to PEDV infection. After the confirmation by western-blot assay, we then investigated the function of these exosomes on PEDV infection and discovered that the exosomes from mock-infected newborn piglets restricted PEDV infection but this inhibition disappeared after exosomes were heat-inactivated, suggesting that the complement is one of the key antiviral molecules. These findings will facilitate the understanding of the antiviral response of the neonate mediated by exosomes
2019-04-30 | PXD010762 | Pride
Project description:To understand the immunomodulatory effects of deoxyshikonin (a natural derivative of well-known Chinese medicine shikonin) on porcine intestinal epithelium cells, the transcriptome analysis was performed to explore the transcriptional profile of porcine IPEC-J2 cells after deoxyshikonin treatment.
2021-11-30 | GSE174377 | GEO