Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global gene expression in response to West Nile virus in mouse spleen and liver

ABSTRACT: Purpose of this experiment was to further understand how innate immune defenses impact host response and West Nile virus tissue tropism. This study examined host-transcriptional response to West Nile virus in permissive and nonpermissive tissues using wildtype mice and mice with genetically altered interferon signaling pathways. Age-matched six to twelve week old mice were inoculated subcutaneously in the left rear footpad with 100 PFU of West Nile virus isolate TX 2002-HC (WNV-TX) in a 10 microL inoculum diluted in Hanks balanced salt solution (HBSS) supplemented with 1% heat-inactivated FBS. Mice were monitored daily for morbidity and mortality. Expression oligonucleotide arrays were performed on RNA isolated from spleen and liver tissues from strain and time-matched mock infected mice (n=2) and WNV-TX infected wild type (WT; n=3; day 4 post-infection), Ips-1-/-(n=3; day 4 post-infection), Ifnar-/- (n=3; day 2 post-infection), and Ips-1-/-xIfnar-/- (DKO; n=3; day 4 post-infection) mice.

ORGANISM(S): Mus musculus

SUBMITTER: Richard Green

PROVIDER: E-GEOD-39259 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of Culex quinquefasciatus responses to WNV infection

Project description:Analysis of Culex quinquefasciatus responses to West Nile virus (WNV) infection at 7 and 14 days after ingestion of infected blood in the gut and carcass tissues. Comparison of WNV-infected to non-infected carcass and gut samples.

2011-11-01 | E-GEOD-23045 | biostudies-arrayexpress

Transcriptional profile of mice with good and poor spatial learning during West Nile virus recovery

Project description:Greater than 50% of patients who survive neuroinvasive West Nile virus (WNV), a mosquito-borne, positive-sense strand flavivirus, exhibit cognitive sequelae including memory impairments which may last several years. High survival rates from WNV neuroinvasive disease (WNND) (>90%) have led to hundreds to thousands of cases of WNV-mediated neurologic impairment accruing annually, yet underlying mechanisms responsible for these impairments have not been investigated. Here, we established a novel murine model of recovery from WNND in which intracranial inoculation of a mutant WNV (WNV-NS5-E218A) leads to rates of survival and cognitive dysfunction that mirror human WNND. WNV-NS5-E218A-recovered mice exhibit impaired spatial learning and persistently phagocytic microglia without significant loss of hippocampal neurons or brain volume. Whole transcriptome analysis of hippocampi from WNV-NS5-E218A-recovered mice with poor spatial learning was performed in order to identify target pathways and molecules underlying cognitive impairments during WNND recovery. Total RNA obtained from isolated murine hippocampus at 25 days post-mock or WNV-NS5-E218A intracranial infection.

2016-06-27 | E-GEOD-72139 | biostudies-arrayexpress

IRF-3, IRF-5, and IRF-7 coordinately regulate the type I IFN response in myeloid dendritic cells downstream of MAVS signaling

Project description:Myeloid dendritic cells from WT, Irf3-/-xIrf7-/-, Irf3-/-xIrf5-/-xIrf7-/-, Mavs-/- (IPS1-/-)and Ifnar-/- mice were infected with West Nile virus to assess the contributions of specific signaling and transcription factors in initiating the antiviral response RPMI + rmGM-CSF purified bone marrow derived myeloid DC (mDC), mock and WNV infected with insect derived virus and RNA isolated at 24 hours post infection . Each genotype has matched mock and infected samples. n=6 for WT mock, WT infected, IFNAR mock, IFNAR infected, IRF3x7 infected; n=5 IRF3x7 infected; n=3 IRF3x5x7 mock, IRF3x5x7 infected, MAVS mock, MAVS infected. RNA was prepared using the Illumina bead station assay and hybridized to Illumina RefSeq-8 V2 BeadChips. Note: MAVS=IPS1

2013-04-23 | E-GEOD-41355 | biostudies-arrayexpress

Mouse popliteal lymph node transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [mRNA]

2016-03-15 | E-GEOD-78888 | biostudies-arrayexpress

Mouse cerebellum transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [WCB001_microRNA]

Project description:The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse cerebellum infected with wild-type West Nile virus (WNV; WNV-NY99 382), and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt). Mice were inoculated with WNV intracranially at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 2 and 4 days post-infection. GSE77161 (WCT001) and this study (WCB001) are 1/4 of cortex and 1/2 of cerebellum from the same mice. Tissues from this experiment are matched to tissues from GSE77161 (WCT001). Infectivity (titer) and pathology are measured from cortex tissue in GSE77161 (WCT001).

2016-02-21 | E-GEOD-77160 | biostudies-arrayexpress

Mouse cortex transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [WCT001_miRNA]

Project description:The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse cortex infected with wild-type West Nile virus (WNV; WNV-NY99 382), and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt). Mice were inoculated with WNV intracranially at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 2 and 4 days post-infection. This study (WCT001) and GSE77160 (WCB001) are 1/4 of cortex and 1/2 of cerebellum from the same mice. Tissues from this experiment are matched to tissues from GSE77160 (WCB001). Infectivity (titer) and pathology are measured from the tissue in WCT001 (i.e., this experiment).

2016-03-12 | E-GEOD-77161 | biostudies-arrayexpress

Mouse cerebellum transcriptome response to a wild type West Nile virus (WNV), New York 99 Strain, and mutant WNV-E218A viruses [WCB001_mRNA]

Project description:The purpose is to obtain samples for mRNA, miRNA, proteomics, lipidomics, metabolomics, and histopathology analysis in mouse cerebellum infected with wild-type West Nile virus (WNV; WNV-NY99 382), and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt). Mice were inoculated with WNV intracranially at a dose of 100 FFU. Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 1, 2, 4, and 6 days post-infection. GSE77193 (WCT001) and this study (WCB001) are 1/4 of cortex and 1/2 of cerebellum from the same mice. Tissues from this experiment are matched to tissues from GSE77193 (WCT001). Infectivity (titer) and pathology are measured from cortex tissue in GSE77193 (WCT001).

2016-02-15 | E-GEOD-77192 | biostudies-arrayexpress

Identification of Antiviral Roles for the Exon-Junction Complex and Nonsense-Mediated Decay in Flaviviral Infection

Project description:West Nile virus (WNV) is an emerging mosquito-borne flavivirus, related to dengue virus and Zika virus. To gain insight into host pathways involved in WNV infection, we performed a systematic affinity-tag purification mass spectrometry (AP-MS) study to identify 259 WNV-interacting human proteins. RNAi screening revealed 26 genes that both interact with WNV proteins and influence WNV infection. We found that WNV, dengue and Zika virus capsids interact with a conserved subset of proteins that impact infection. These include the exon-junction complex (EJC) recycling factor, PYM1, which is antiviral against all three viruses. The EJC has roles in nonsense-mediated decay (NMD), and we found that both the EJC and NMD are antiviral. Mechanistically, we found that the EJC protein RBM8A directly binds WNV RNA. To counteract this antiviral defense, flavivirus infection inhibits NMD and the interaction of capsid with PYM1 interferes with EJC protein function and localization. Moreover, depletion of PYM1 attenuates RBM8A binding to viral RNA, suggesting that WNV sequesters PYM1 to protect viral RNA from decay. Together, these data suggest a complex interplay between the virus and host in regulating NMD and the EJC complex.

2019-11-14 | PXD011728 | Pride

Gene Expression Analysis in the Thalamus and Cerebrum of Horses Experimentally Infected with West Nile Virus

Project description:The purpose of this experiment was to further our understanding of gene expression in the central nervous system (thalamus and cerebrum) after exposure to West Nile virus. To that end, three different analyses were performed. The first examined differences in gene expression between horses not vaccinated and exposed to WNV and normal control horses (exposure). The second examined differences in gene expression between horses not vaccinated and exposed to WNV and horses vaccinated and exposed to WNV (survival). And the third examined differences between the nonvaccinated cerebrum and nonvaccinated thalamus of horses exposed to WNV (location). Six conditions- Gene expression in the thalamus and cerebrum of three different groups of horses (Non-vaccinated horses exposed to West Nile virus, Vaccinated horses exposed to West Nile virus, normal horses not exposed to West Nile virus). Biological replicates- 6 normal cerebrums, 6 normal thalamus, 6 vaccinated and exposed cerebrums, 6 vaccinated and exposed thalamus, 6 non-vaccinated and exposed cerebrum, 6 non-vaccinated and exposed thalamus.

2011-08-31 | E-GEOD-30347 | biostudies-arrayexpress

Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis

Project description:Background: West Nile virus is an emerging infection of biodefense concern and there are no available treatments or vaccines. Here we used a high-throughput method based on a novel gene expression analysis, RNA-Seq, to give a global picture of differential gene expression by primary human macrophages of 10 healthy donors infected in vitro with WNV. Results: From a total of 50 million reads per sample, we employed a Bayesian hierarchical mixture model to identify 4,026 transcripts that were differentially expressed after infection. Both predicted and novel gene changes were detected, as were gene isoforms, and while many of the genes were expressed by all donors, some were unique. Knock-down of genes not previously known to be associated with WNV resistance identified their critical role in control of viral infection. Conclusions: Our study distinguishes both common gene pathways as well as novel cellular responses. Such analysis will be valuable for translational studies of susceptible and resistant individuals -- and for targeting therapeutics -- in multiple biological settings. Differential gene expression by primary human macrophages of 10 healthy donors infected in vitro with WNV were generated by RNA-Seq.

2014-01-08 | E-GEOD-40718 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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