E-MTAB-76
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-76 | ExpressionAtlas | 2015-10-30
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:The underlying pathogenic mechanisms of prion infection are not well characterized. To study the effect of prion infection on gene expression in neuronal cell cultures, a neuroblastoma (N2a) cell clone was infected with either the mouse adapted prion strain 22L or exposed to uninfected brain homogenate as a negative control. Large scale expression analysis was performed using a cDNA microarray chip comprising about 21,000 spotted ESTs. Over hundred genes were identified that are differentially expressed in 22L-infected cells when compared to uninfected cells. Several of the identified changes in gene expression have also been reported for other neurodegenerative diseases such as Alzheimer`s disease. Keywords: cDNA arrays, prion, N2a, neuroblastoma cell line, murine A neuroblastoma (N2a) cell clone was infected with either the mouse adapted prion strain 22L or exposed to uninfected brain homogenate as a negative control. Eight replicates including four dye swap experiments have been performed for the comparison of prion infected cells versus control cells.
2010-05-26 | E-GEOD-7119 | biostudies-arrayexpress
Project description:Prions cause transmissible neurodegenerative diseases and replicate by conformational conversion of normal, benign forms of prion protein (PrPC) to disease-causing PrPSc isoforms. A systems approach to disease postulates that disease arises from the pathological perturbation (genetic and/or environmental) of one or more biological networks in the relevant organ. In this regard, we tracked global (all mRNA transcripts) gene expression in the brains of eight distinct mouse strain-prion strain combinations at 8 - 10 time points throughout the progression of the disease to capture the effects of prion strain, host genetics, and PrP concentration on disease incubation time. Data are also available from http://prion.systemsbiology.net
2009-03-25 | E-MTAB-76 | biostudies-arrayexpress
Project description:To uncover links between metabolism and disease severity in murine malaria, we performed plasma metabolomics via Metabolon on eight inbred, Plasmodium chabaudi-infected mouse strains with diverse disease phenotypes. We sacrificed and collected plasma from >=3 mice per strain per day of acute infection alongside uninfected control mice (approximately days 5-12 depending on mouse strain). We collected disease severity data, e.g. weight loss, liver enzymes, and anemia, concurrently. Together, these data enable 1) a picture of strain-specific and conserved metabolic responses during acute malaria, and 2) a comparison between metabolic responses and disease severity.
2021-04-11 | ST001775 | MetabolomicsWorkbench
Project description:The overall goal of the study was to use in vivo data combined with functional genomics to define gene expression signatures representative of a spectrum of HSV CNS infections. Innate immune deficiencies result in a spectrum of severe clinical outcomes following infection. In particular, there is a strong association between loss of the signal transducer and activator of transcription (Stat) pathway, breach of the blood-brain barrier (BBB), and virus-induced neuropathology. The gene signatures that characterize resistance, disease, and mortality in the virus-infected nervous system have not been defined. Herpes simplex virus type 1 (HSV-1) is commonly associated with encephalitis in humans, and humans and mice lacking Stat1 display increased susceptibility to HSV central nervous system (CNS) infections. In this study, two HSV-1 strains were used, KOS (wild type [WT]), and Δvhs, an avirulent recombinant lacking the virion host shutoff (vhs) function. In addition, two mouse strains were used: strain 129 (control) and a Stat1-deficient (Stat1(-/-)) strain. Using combinations of these virus and mouse strains, we established a model of infection resulting in three different outcomes: viral clearance without neurological disease (Δvhs infection of control mice), neurological disease followed by viral clearance (Δvhs infection of Stat1(-/-) mice and WT infection of control mice), or neurological disease followed by death (WT infection of Stat1(-/-) mice). Through the use of functional genomics on the infected brain stem and liver, we determined gene signatures that were representative of the three infection outcomes. Gender matched, 6- to 8- week old immunocompetent, control 129S6 and 129S6 Stat1 knockout mice were infected corneally with 2x10^6 PFU of either wild type HSV-1, a vhs-null HSV virus, or mock-infected. Brain stems and liver of individual mice were isolated at days 1, 3, 5 and 7 post-inoculation for microarray analysis. For microarray analysis, samples were collected from n=2 animals (1 male, 1 female) per mouse strain and virus strain for each time point. Equal masses of tissue were pooled from two mock-infected mice per time point and run on microarray.
2012-02-21 | E-GEOD-35943 | biostudies-arrayexpress
Project description:West Nile virus (WNV) and Chikungunya virus (CHIKV) are arboviruses that are constantly (re)-emerging and expanding their territory. Both viruses often cause a mild form of disease, but severe forms of the disease can consist of neurological symptoms, most often observed in young children and the elderly, which are poorly understood. To elucidate the mechanisms responsible for end-stage WNV and CHIKV neuroinvasive disease and pathogenesis, we used transcriptomics to compare the effector pathways in the brain during the early and late stage of disease in young mice. Mice were infected with WNV strain NY99 (accession AF196835.2, obtained from the Health Protection Agency, Porton Down, UK; P5 on Vero E6 cells) or CHIKV strain S27, accession AF369024). Nine-day old female C57/BL6 mice were inoculated intraperitoneally with either 10^5 TCID50/100 µL of WNV-NY99 (n=6) or 10^6.5 TCID50/100 µL of CHIKV-S27 (n=6), or mock-infected. Mice were sacrificed 2, 3 or 5 days post-innoculation depending on the virus. For transcriptomic analysis, cerebellum was separated from the brain and the right hemisphere was gently washed once in ice-cold PBS and stored in RNAlater® (Thermo Fisher Scientific, Bleiswijk, The Netherlands) until further processing. Total RNA was isolated from the brain samples using Trizol Reagentand the RNEasy Mini kit. RNA (200 ng) was labeled using the MessageAmp Premier RNA Amplification kit (Applied Biosystems) and hybridized to Affymetrix GeneChip® Mouse 4302 Arrays. Image analysis was performed using GeneChip Operating Software. Microarray Suite version 5.0 software (Affymetrix) was used to generate .dat and .cel files for each experiment. Using this approach, we find evidence for a strong inflammatory response was found in mice infected with WNV and CHIKV. The transcriptomics profile measured in mice with WNV and CHIKV neuroinvasive disease in our study showed strong overlap with the mRNA profile described in the literature for other viral neuroinvasive diseases.
2017-08-17 | E-MTAB-5832 | biostudies-arrayexpress
Project description:The interplay between the Apicomplexan parasite Toxoplasma gondii and its host has been largely studied. However, molecular changes at the metabolic level in the host central nervous system and pathogenesis-associated metabolites during brain infection are largely unexplored. We used a global metabolomics strategy to identify differentially regulated metabolites and affected metabolic pathways in BALB/c mice during infection with T. gondii Pru strain at 7, 14 and 21 days post-infection (DPI). The non-targeted Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics analysis detected approximately 2,755 retention time-exact mass pairs, of which more than 60 had significantly differential profiles at different stages of infection. These include amino acids, organic acids, carbohydrates, fatty acids, and vitamins. The biological significance of these metabolites is discussed. Principal Component Analysis and Orthogonal Partial Least Square-Discriminant Analysis showed the metabolites’ profile to change over time with the most significant changes occurring at 14 DPI. Correlated metabolic pathway imbalances were observed in carbohydrate metabolism, lipid metabolism, energetic metabolism and fatty acid oxidation. Eight metabolites correlated with the physical recovery from infection-caused illness were identified. These findings indicate that global metabolomics adopted in this study is a sensitive approach for detecting metabolic alterations in T. gondii-infected mice and generated a comparative metabolic profile of brain tissue distinguishing infected from non-infected host.
2017-01-27 | MTBLS217 | MetaboLights
Project description:The overall goal of the study was to use in vivo data combined with functional genomics to define gene expression signatures representative of a spectrum of HSV CNS infections. Innate immune deficiencies result in a spectrum of severe clinical outcomes following infection. In particular, there is a strong association between loss of the signal transducer and activator of transcription (Stat) pathway, breach of the blood-brain barrier (BBB), and virus-induced neuropathology. The gene signatures that characterize resistance, disease, and mortality in the virus-infected nervous system have not been defined. Herpes simplex virus type 1 (HSV-1) is commonly associated with encephalitis in humans, and humans and mice lacking Stat1 display increased susceptibility to HSV central nervous system (CNS) infections. In this study, two HSV-1 strains were used, KOS (wild type [WT]), and Δvhs, an avirulent recombinant lacking the virion host shutoff (vhs) function. In addition, two mouse strains were used: strain 129 (control) and a Stat1-deficient (Stat1(-/-)) strain. Using combinations of these virus and mouse strains, we established a model of infection resulting in three different outcomes: viral clearance without neurological disease (Δvhs infection of control mice), neurological disease followed by viral clearance (Δvhs infection of Stat1(-/-) mice and WT infection of control mice), or neurological disease followed by death (WT infection of Stat1(-/-) mice). Through the use of functional genomics on the infected brain stem and liver, we determined gene signatures that were representative of the three infection outcomes.
2012-02-21 | GSE35943 | GEO
Project description:Viral infections of the central nervous system cause acute or delayed neuropathology and clinical consequences ranging from asymptomatic courses to chronic, debilitating diseases. The outcome of viral encephalitis is partially determined by genetically programmed immune response patterns of the host. Experimental infection of mice with Theiler’s murine encephalomyelitis virus (TMEV) causes diverse neurologic diseases, including TMEV-induced demyelinating disease (TMEV-IDD), depending on the used mouse strain. The aim of the present study was to compare initial transcriptomic changes occurring in the brain of TMEV-infected SJL (TMEV-IDD susceptible) and C57BL/6 (TMEV-IDD resistant) mice. Animals were infected intracerebrally with TMEV and sacrificed 4, 7 or 14 days post infection (dpi). Control animals of both strains were inoculated with vehicle only and sacrificed at 7 dpi. RNA was isolated from brain tissue and analyzed by whole transcriptome sequencing. Selected differences were confirmed on a protein level by immunohistochemistry. In mock-infected mice SJL and C57BL/6 mice, >200 differentially expressed genes (DEGs) were detected. Following TMEV-infection, the number of DEGs increased to >700. Infected C57BL/6 mice showed a higher expression of transcripts related to antigen presentation MHCI I, innate antiviral immune responses and cytotoxicity, compared to infected SJL animals. Many of those genes were also upregulated in SJL mice upon infection, but the response was weaker or delayed, which could be responsible for failure of viral clearance in this mouse strain. SJL mice showed prolonged elevation of MHC II and chemotactic genes, compared to C57BL/6 mice, which presumably facilitates the induction of chronic demyelinating disease. In addition, elevated expression of several genes associated with immunomodulatory or –suppressive functions was observed in SJL mice. The exploratory study confirms previous observations in the model and provides an extensive list of immunologic parameters potentially contributing to different outcomes of viral encephalitis in two mouse strains.
2020-12-15 | GSE159226 | GEO
Project description:WGS and WGBS data from monocyte-derived macrophages that were infected with Influenza A virus strain PR8WT, or a matching non-infected control.
| EGAD00001008359 | EGA
Project description:A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease
| PRJNA593734 | ENA