Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1188728 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31418894.fastq.gz | Fastqsanger.gz | |||
| SRR31418895.fastq.gz | Fastqsanger.gz | |||
| SRR31418896.fastq.gz | Fastqsanger.gz | |||
| SRR31418897.fastq.gz | Fastqsanger.gz | |||
| SRR31418898.fastq.gz | Fastqsanger.gz |
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Project description:Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus and causes acute encephalitis with high mortality rate in humans. Despite the demonstration of difference in neuroinvasiveness between JEV strains, little is known about host gene response upon infection of virulent and attenuated JEV strains. To understand the pathogenesis mechanism of JEV infection, we performed a comparative genome-wide microarray analysis (Affymetrix, mouse genome 430 2.0 with 45101 probe sets) of genes expressed in the mice brains three days post intracerebrally inoculated with JEV strains of different neurovirulence. We found that the virulent strain of JEV (RP-9) tended to affect the host gene expression more profoundly than the attenuated one (RP-2ms), as 961 vs. 665 and 655 vs. 509 genes were at least two-fold upregulated and downregulated by RP-9 and RP-2ms, respectively. In order to understand the host defense response against JEV, we further analyzed the microarray data with special focus on immune response. The expression levels of selected genes were further verified by quantitative RT-PCR at 1-, 3- and 5-day post JEV infection. The differentially regulated genes reported here likely contribute to the neurovirulent phenotype by modulating the host immunity, viral replication and/or cytotoxicity. Keywords: day3, virus (1 x 10^4 PFU), intracerebrally (ic) inoculated, brain total RNA
2021-10-01 | GSE9524 | GEO
Project description:Japanese encephalitis virus (JEV), a member of the Flaviviridae family, is a leading cause of viral encephalitis in humans. Survivors of this infection often develop life-long neurological sequelae. Short-chain fatty acids (SCFAs) produced in the gut are vital mediators of the gut-brain axis. We aimed to study microRNA-based mechanisms of SCFAs in an in vitro model of JEV infection. N9 microglial cells were pre-treated with SCFA cocktail before JEV infection. Cytokine bead analysis (CBA), immunoblotting and PCR were performed to analyse relevant inflammatory markers. microRNA sequencing was performed using Illumina Hiseq and Bioinformatical tools were used for differentially expressed (DE) miRNAs and Weighted gene co-expression network analysis (WGCNA). microRNA mimic/inhibitor experiments and luciferase assay were performed to study miRNA-target interaction. A significant reduction in MCP1 and TNFα along with reduced expression of phospho-NF-κB was observed in SCFA conditions. Significant attenuation of HDAC activity and protein expression was recorded. miRNA sequencing revealed 160 DE miRNAs in SCFA+JEV treated cells at 6 hours post infection (HPI). WGCNA revealed miR-200a-3p, a hub miRNA significantly upregulated in SCFA conditions. Transcription factor ZBTB20 was bioinformatically predicted and validated as a gene target for miR200a-3p. Further miRNA mimic/inhibitor assay demonstrated that miR-200-3p regulated ZBTB20 along with Iκβα that possibly dampened NF-κB signal activation downstream.
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Project description:B16F10, a murine melanoma cel line is cytolytic to JEV infection. We have identified a B16F10 cell line variant which is non-cytolytic to JEV infection. This variant cell line has two types of cells, one which is persistently infected JEV and another which is resistant to JEV infection. The JEV-resistant cells (B16F10r) were seperated from the presistently infected cells by single cell cloning. To understand the mechanism of JEV resistance microarray analysis was caried out to Identify and characterize genes differentially expressed during in uninfected/JEV-infected B16F10 and B16F10r cells.
2013-08-01 | GSE42942 | GEO
Project description:CHME3 cells grown on six-wells were infected with Japanese encephalitis virus (JEV) (P20778 strain), and total RNA was isolated from cells at 6, 24 and 48 h of post infection. MicroRNA expression was significantly altered in JEV-infected human microglial cells. A time-dependent change in microRNA profile was noted. Bioinformatics analysis identified anti-correlation between differentially expressed miRNAs and the gene expression at different time point which ultimately affected several signalling pathways in microglia cells. Brain-enriched microRNAs and a set of microRNA previously designated as NeurimmiRs were also differentially expressed in response to JEV infection.
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Project description:Japanese encephalitis (JE) is an acute encephalitis syndrome contributed to Japanese encephalitis virus (JEV) infection. It is the chief cause of viral encephalitis in Asian. In recent years, association of JEV infection with neurological problems such as Guillain-Barré syndrome had reported. Nevertheless, its potential pathogenic mechanism has never been reported. Therefore, it is urgent to explore the relationship between peripheral nerve injury and JEV infection. Here, we use the liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique to make out the protein expression levels of mice sciatic nerve between JEV infection group and the sham group. In general, 4303 proteins were identified by MS, and 187 differentially expressed proteins were found. There were 105 proteins up-regulated in the injured sciatic nerve, and 82 proteins were down-regulated. Functional enrichment analysis of differentially expressed proteins showed that the up-regulated proteins were mainly related to immune regulatory response, and the down-regulated proteins were related to ribosomal structural components and translation.
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Project description:B16F10, a murine melanoma cel line is cytolytic to JEV infection. We have identified a B16F10 cell line variant which is non-cytolytic to JEV infection. This variant cell line has two types of cells, one which is persistently infected JEV and another which is resistant to JEV infection. The JEV-resistant cells (B16F10r) were seperated from the presistently infected cells by single cell cloning. To understand the mechanism of JEV resistance microarray analysis was caried out to Identify and characterize genes differentially expressed during in uninfected/JEV-infected B16F10 and B16F10r cells. Agilent one-color experiment,Organism: Mus musculus ,Agilent Custom Mouse Whole Genome Mouse 8x60k Gene expression designed by Genotypic Technology Private Limited, Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
2013-08-01 | E-GEOD-42942 | biostudies-arrayexpress
Project description:CHME3 cells grown on six-wells were infected with Japanese encephalitis virus (JEV) (P20778 strain), and total RNA was isolated from cells at 6, 24 and 48 h of post infection. MicroRNA expression was significantly altered in JEV-infected human microglial cells. A time-dependent change in microRNA profile was noted. Bioinformatics analysis identified anti-correlation between differentially expressed miRNAs and the gene expression at different time point which ultimately affected several signalling pathways in microglia cells. Brain-enriched microRNAs and a set of microRNA previously designated as NeurimmiRs were also differentially expressed in response to JEV infection. CHME3 cells grown on 6-well plate. Three replicates of uninfected and JEV-infected samples at each time point (6, 24 and 48 h of post infection) were used for microRNA array.
2015-01-01 | E-GEOD-57410 | biostudies-arrayexpress
Project description:CHME3 cells grown on six-wells were infected with Japanese encephalitis virus (JEV) (P20778 strain ) and total RNA was isolated from cells at 6, 24 and 48 h of post infection mRNA expression was significantly altered in JEV infected human microglial cells. A time dependant change in microRNA profile was noted. Bioinformatics analysis identified anti correlation between differentially expressed miRNAs and the gene expression at different time point which ultimately affected several signalling pathways in microglia cells. Brain enriched microRNAs and a set of microRNA previously designated as NeurimmiRs were also differentially expressed in response to JEV infection
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Project description:In order to further determine the je virus (JEV) infection in C57BL / 6 mice after its miRNA levels change, we use the Agilent micrornas chip as a platform, to detect the uninfected group (control group) and the experimental mouse total RNA, it is found that the miRNA levels decrease infection group, and picked out the ten changes obviously micrornas verification, the result is the same.
2020-04-04 | GSE148030 | GEO