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Sus scrofa

ABSTRACT: Transcriptome sequencing of IPEC-J2 cells infected with PEDV

PROVIDER: PRJNA633864 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11815056_1.fastq.gz	Fastqsanger.gz
	SRR11815056_2.fastq.gz	Fastqsanger.gz
	SRR11815057_1.fastq.gz	Fastqsanger.gz
	SRR11815057_2.fastq.gz	Fastqsanger.gz
	SRR11815058_1.fastq.gz	Fastqsanger.gz

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Identification of cell types and transcriptome landscapes of PEDV infected porcine small intestine using single-cell RNA-sequencing

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.

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Transcriptome-wide m6A methylome of intestinal porcine epithelial cells (IPEC-J2) induced by deoxynivalenol

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.

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Project description:IVT-SAPAS sequencing of IPEC-J2 cells infected or mock infected PEDV

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Project description:Sus scrofa IPEC-J2 cell lncRNA Raw sequence reads

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Project description:H2O2-induced oxidative stress model of IPEC-J2 and treatment with peptides

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