Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CRISPR screening of porcine sgRNA library identifies host factors associated with Japanese encephalitis virus replication

ABSTRACT: We design a porcine genome-scale CRISPR/Cas9 knockout (PigGeCKO) library containing 85,674 single guide RNAs targeting 17,743 protein-coding genes, 11,053 long ncRNAs, and 551 microRNAs. Subsequently, we use the PigGeCKO library to identify key host factors facilitating JEV infection in porcine cells.

ORGANISM(S): Sus scrofa

PROVIDER: GSE158247 | GEO | 2020/09/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CRISPR screening of porcine sgRNA library identified host factors facilitating Japanese encephalitis virus replication

Project description: Not available

| S-BSST510 | biostudies-other

CRISPR screening of porcine sgRNA library identifies host factors associated with Japanese encephalitis virus replication.

Project description:Japanese encephalitis virus (JEV) is a mosquito-borne zoonotic flavivirus that causes encephalitis and reproductive disorders in mammalian species. However, the host factors critical for its entry, replication, and assembly are poorly understood. Here, we design a porcine genome-scale CRISPR/Cas9 knockout (PigGeCKO) library containing 85,674 single guide RNAs targeting 17,743 protein-coding genes, 11,053 long ncRNAs, and 551 microRNAs. Subsequently, we use the PigGeCKO library to identify key host factors facilitating JEV infection in porcine cells. Several previously unreported genes required for JEV infection are highly enriched post-JEV selection. We conduct follow-up studies to verify the dependency of JEV on these genes, and identify functional contributions for six of the many candidate JEV-related host genes, including EMC3 and CALR. Additionally, we identify that four genes associated with heparan sulfate proteoglycans (HSPGs) metabolism, specifically those responsible for HSPGs sulfurylation, facilitate JEV entry into porcine cells. Thus, beyond our development of the largest CRISPR-based functional genomic screening platform for pig research to date, this study identifies multiple potentially vulnerable targets for the development of medical and breeding technologies to treat and prevent diseases caused by JEV.

| S-EPMC7560704 | biostudies-literature

CRISPR screening of porcine sgRNA library identifies host factors associated with Japanese encephalitis virus replication

Project description:CRISPR screening of porcine sgRNA library identifies host factors associated with Japanese encephalitis virus replication

| PRJNA664556 | ENA

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

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

Host Genes Differentially Expressed by Virulent and Attenuated Strains of Japanese Encephalitis Virus

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

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

2015-01-01 | E-GEOD-57330 | 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

2015-01-01 | GSE57330 | GEO

Global gene expression profile of Japanese encephalitis virus(JEV) infected cytolytic B16F10 and Non-cytolytic JEV resistant B16F10r

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

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