Dataset Information

Integrated analysis of mRNAs and lncRNAs repertoires involved immune response in panleukopenia virus-infected feline kidney cell line

ABSTRACT: Integrated analysis of mRNAs and lncRNAs repertoires involved immune response in panleukopenia virus-infected feline kidney cell line

PROVIDER: PRJNA573728 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	SRR10166469_1.fastq.gz	Fastqsanger.gz
	SRR10166469_2.fastq.gz	Fastqsanger.gz
	SRR10166470.fastq.gz	Fastqsanger.gz
	SRR10166470_1.fastq.gz	Fastqsanger.gz
	SRR10166470_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 15

Similar Datasets

Project description:Purporse: FPV can cause a viral disease that occurs in cats, causing severe leukopenia, gastro-enteritis and nervous signs and leads to significant losses. LncRNAs biochemically resemble mRNAs posited by Jacob and Monod, yet do not template protein synthesis. Rather, lncRNAs functioning as RNA genes to play an important role in many biological and pathological processes such as inflammation and viral infection. However, lncRNAs have not been comprehensively identified in felines. Here, microarrays of mRNAs and lncRNAs were globally performed to identify the lncRNAs related to immune response of feline panleukopenia virus infection in F81 cells. Methods:lncRNA and mRNA sequencing analysis was performed on an Illumina Hiseq 4000 (LC Sciences, USA) following the vendor's recommended protocol Results: Through RNA sequencing, we performed a comprehensive analysis of lncRNAs and mRNAs in FPV infected F81 cells. F81 cells infected or uninfected FPV were used to prepare six libraries to generate 14.66 to 15.45 gigabytes (GB) clean reads per sample. We obtained 90588 novel lncRNAs, and 291 are differential expressed lncRNAs between FPV infected cells and uninfected cells. Consistent with previous studies, lncRNAs showed features distinct from mRNAs, such as shorter lengths, lesser exon numbers, and lower expression levels compared to mRNAs. The GO enrichment and KEGG pathway analyses showed that a majority of genes and lncRNAs were mainly related to the immune response of host cells with FPV infection. By differentially expressed target genes as well as co-expression network construction analysis, 21 key differentially expressed genes (19 upregulated & 2 downregulated) related to immune regulation of FPV infection in F81 cells were identified. Moreover, fifteen differentially expressed genes (five lncRNAs, ten mRNAs) were selected and independently validated by reverse-transcription qPCR and the results were consistent with the sequencing results. Conclusion: The present study is the first to provide insights into the biological connection of lncRNAs and FPV infection, which can be further explore for the potential link between lncRNA expression and the pathogenesis of FPV infection.

Project description:Purpose: Marek's disease virus (MDV) is an oncogenic herpesvirus that can induce T-cell lymphoma. Long noncoding RNA (lncRNA) strongly associated with various cancers and many other diseases. In chickens, lncRNAs have not been comprehensively identified. Here, we profiled mRNA and lncRNA repertoires in three groups of spleens from MDV-infected and non-infected chickens, including seven tumorous spleens (TS) from MDV-infected chickens, five spleens from the survivors (SS) without any lesion after MDV infection, and five noninfected spleens (NS) from chickens, to explore the underlying mechanism of host resistance to Marek's disease (MD). Results: By using precise lncRNA identification pipeline, we identified 1315 putative lncRNAs and 1166 known lncRNAs in spleen tissue. Genomic features of putative lncRNAs were characterized. Differentially expressed mRNAs, putative lncRNAs and known lncRNAs were profiled. Some previously reported MD resistance candidate genes, such as CTLA4, HDAC9 and CD72, were also found in our differentially expressed genes list. Moreover, we found that several intergroup specifically deregulated genes were involved in important biological processes and pathways, including B cell activation and Wnt signaling pathway. We conducted co-expression network using WGCNA and identified several hub genes that may play pivotal roles in MD resistance and tumorigenesis, e.g. CTLA4, SWAP70, CXCL12 and JCHAIN. According to the expression relationship between lncRNAs and MD resistance candidate mRNAs, five deregulated lncRNAs may implicate the chicken immunity by directly or indirectly regulating those hub genes. Conclusions: We profiled both lncRNA and mRNA expression patterns in MDV-infected chicken spleens. Expression variations of intergroup specifically deregulated genes engaged in important immune process likely contributed to robust immune system in the survivors. Some oncogenesis or MD resistance related genes deregulated between groups, like CTLA4, HDAC9 and CD72 were found. Co-expression network analysis manifested that lncRNAs may affect MD resistance and tumorigenesis in chicken spleens through their impact on expression of CTLA4, SWAP70 and some other genes that are critical in many important biological processes, such as B lymphocyte proliferation and activation.

Dataset Information

Integrated analysis of mRNAs and lncRNAs repertoires involved immune response in panleukopenia virus-infected feline kidney cell line

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets