Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

43 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA expression profile in CHME3 cells infected with Japanese encephalitis virus

ABSTRACT: 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 Cells grown on 6-well well plate. Three replicates of uninfected and infected samples at each time point was used for mRNA experiment.

ORGANISM(S): Homo sapiens

SUBMITTER: ARUP BANERJEE

PROVIDER: E-GEOD-57330 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

MicroRNA expression profile in CHME3 cells infected with Japanese encephalitis virus

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

MicroRNA expression profile in CHME3 cells infected with Japanese encephalitis virus

2015-01-01 | GSE57410 | GEO

mRNA expression profile in CHME3 cells infected with Japanese encephalitis virus

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

2015-01-01 | GSE57330 | GEO

Gene expression profile in Caco-2 cells infected with Japanese encephalitis virus

Project description:Caco-2 cells grown on transwells were infected with Japanese encephalitis virus (JEV) and total RNA was isolated from cells at the time when trans-epithelial electrical resistance was reduced by about 50% of uninfected cells

2019-12-31 | GSE39740 | GEO

Ribosome profiling of Japanese encephalitis virus infected Neuro2a cells

Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of mouse neuroblastoma (Neuro2a) cells infected with Japanese Encephalitis Virus (JEV) P20778 Vellore strain. At 18 h post infection (p.i.), infected cells were treated with either cycloheximide (translation elongation inhibitor) or in combination with harringtonine (translation initiation inhibitor). Ribo-Seq libraries were prepared using a broad range of fragment lengths (25 to 70 nucleotides) and deep sequenced. This allowed for estimation of ribosomal frameshifting efficiency and discovery of a novel upstream open reading frame (uORF) in JEV along with perturbations in ribosome-associated tRNA levels upon JEV infection.

2021-07-05 | E-MTAB-9352 | biostudies-arrayexpress

Analyses of Long Non-coding RNA and mRNA Profiles using Microarray Platform in Mice Brain during Japanese Encephalitis Virus Infection

Project description:Japanese encephalitis virus (JEV) is the leading cause of epidemic encephalitis worldwide. JEV-induced neuroinflammation is characterized by profound neuronal cells damage accompanied by activation of glial cells. Albeit long non-coding RNAs (lncRNAs) have been emerged as important regulatory RNAs with profound effects on various biological processes, it is unknown how lncRNAs regulate JEV-induced inflammation. Here, using microarray approach, we identified 618 lncRNAs and 1007 mRNAs differentially expressed in JEV-infected mice brain.

2017-02-11 | GSE94789 | GEO

Transcriptome Profiling of Japanese Encephalitis Virus (JEV) Infected Human Neuroepithelioma Cells (SK-N-MC)

Project description:Japanese Encephalitis (JE) is an important causal of viral encephalitis in Eastern and Southeast Asia. Neuronal injury and varying degrees of neuroinflammation are often pathological hallmarks of JE, which result in high morbility and mortality rates. However, a clear understanding on neuron cells' responses to JEV infection remains elusive. This study, therefore, utilized the Affymetrix Human PrimeView array for a robust profiling of JEV infected SK-N-MC cells during the active phase of infection in order to investigate the molecular details of the host cell responses.

2018-11-20 | GSE115167 | GEO

Comparison of the Human Neuronal Proteome upon Japanese Encephalitis or West Nile Virus Infection and potential role of mosquito saliva in neuropathogenesis

Project description:Neurotropic flavivirus Japanese encephalitis virus (JEV) and West Nile virus (WNV) are amongst the leading causes of encephalitis. Using label-free quantitative proteomics, we identified proteins differentially expressed upon JEV (gp-3, RP9) or WNV (IS98) infection of human neuroblastoma cells. Both viruses were associated with the up-regulation of immune response (IFIT1/3/5, ISG15, OAS, STAT1, IRF9) and the down-regulation of SSBP2, involved in gene expression, as well as PAM, involved in neuropeptide amidation. Proteins associated to membranes, involved in extracellular matrix organization and collagen metabolism represented major clusters down-regulated by JEV and WNV. Moreover, transcription regulation and mRNA processing clusters were also heavily regulated by both neurotropic flaviviruses. If the proteome of neuroblastoma cells infected by JEV or WNV was significantly modulated in the presence of mosquito saliva, both viruses showed distinct patterns. Mosquito saliva favored the modulation of proteins associated with gene regulation in JEV infected neuroblastoma cells while it was the modulation of proteins associated with protein maturation, signal transduction and ion transporters in the case of WNV infected neuroblastoma cells.

2020-05-14 | PXD016805 | Pride

Short-chain fatty acids abrogate Japanese encephalitis virus-induced inflammation in microglial cells via miR200a-3p/ZBTB20/Ikβα axis

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.

2024-05-20 | GSE267173 | GEO

Label-Free Proteomics-based analysis of peripheral nerve injury induced by Japanese encephalitis virus

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.

2022-05-27 | PXD030128 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data