Chicken Macrophage RNAseq MDV Infected/Control
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB29321 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2855720_1.fastq.gz | Fastqsanger.gz | |||
| ERR2855720_2.fastq.gz | Fastqsanger.gz | |||
| ERR2855730_1.fastq.gz | Fastqsanger.gz | |||
| ERR2855730_2.fastq.gz | Fastqsanger.gz | |||
| ERR2855721_1.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional profiling of chicken spleen tissues from Marek's disease virus (MDV) infected and non-infected control individuals from three inbred chicken lines 63, 72, RCSM with varying disease resistance characteristics. Line 63 is highly resistant; line 72 is highly susceptible; and line RCSM has intermediate resistance. Our goal was to investigate the genetic basis of systemic variation in disease resistance in these genetically similar individuals. Three time points were chosen at different stages of disease progression - 5 days post-infection (dpi) - early cytolytic phase; 10 dpi - latent phase; and 21 dpi - late cytolytic phase with 4 replicates at each stage.
2010-09-08 | GSE24017 | GEO
Project description:Transcriptional profiling of chicken spleen tissues from Marek's disease virus (MDV) infected and non-infected control individuals from three inbred chicken lines 63, 72, RCSM with varying disease resistance characteristics. Line 63 is highly resistant; line 72 is highly susceptible; and line RCSM has intermediate resistance. Our goal was to investigate the genetic basis of systemic variation in disease resistance in these genetically similar individuals. Three time points were chosen at different stages of disease progression - 5 days post-infection (dpi) - early cytolytic phase; 10 dpi - latent phase; and 21 dpi - late cytolytic phase with 4 replicates at each stage. Two-condition experiment, MDV infected sample vs non-infected control, 3 chicken lines - 63, 72 and RCSM, 3 time points - 5, 10 & 21 dpi. Biological replicates: 4 non-infected control replicates, 4 infected replicates for each line at each time point.
2010-09-08 | E-GEOD-24017 | biostudies-arrayexpress
Project description:Using global transcriptome analysis and specific pathogen free chicken CEF, we try to identify genes, pathways involving in the response to MDV infection.
2016-04-30 | GSE59052 | GEO
Project description:B lymphocytes from the chicken Bursa of Fabricius were isolated and cultured in the presence of CD40L. Cells were infected with a GFP fluorescent reporter virus of the very virulent Marek's disease virus (vvMDV) strain RB-1B (RB-1B_UL47-GFP, see doi: 10.1073/pnas.1424420112). After 24h viable infected (GFPpositive) and uninfected (GFPnegative) B-cells were sort purified from these cultures. Viable B cells, purified from uninfected cultures served as control. 3x10^6 cells per sample were subjected to RNA isolation and microarray analysis. Goal of the experiment was to elucidate the reaction of chicken B cells, primary target cells of MDV upon infection with this virus.
2021-07-10 | E-MTAB-10702 | biostudies-arrayexpress
Project description:Marek's disease virus (MDV) is a highly contagious oncogenic herpes virus. Classed as an alpha herpes virus due to its DNA sequence and genome organization, its biological properties are more similar to those of gamma herpes viruses. MDV causes an initial cytolytic infection in B lymphocytes (3-6dpi) followed by infection of CD4+ T cells (at around 7dpi) where the virus becomes latent (for around two weeks) and then goes on to produce lymphoid tumours in the skin, nerves and internal organs. Early symptoms in susceptible birds include lameness, paralysis, loss of appetite, depression, blindness and immuno-suppression. The route of infection is usually respiratory and the disease is highly contagious, being spread by infective feather-follicle dander. Although birds may survive MDV infection, the resultant immuno-suppression leaves the birds highly susceptible to other infections. MDV infection can thus be associated with high mortality rates and, in turn, large economic losses throughout the worldï¾Âs poultry industry. Three-week-old chicks were inoculated with virus (RB1B) via an intra-gastric route and tissue samples were collected at 2, 3 and 4 days post-inoculation. Spleen and thymus tissue were examined from control and infected birds at 2, 3 and 4 days post-infection in birds known to be either susceptible or resistant to the virus. As well as understanding the host immune response to MDV, we are interested in identifying genes involved in disease resistance and so we have analysed the gene expression profiles at these times, when the innate immune response is active. We assume that genes underlying resistance will be involved at this early stage of the host immune response.
2010-12-31 | E-TABM-721 | biostudies-arrayexpress
Project description:Background: Marek’s disease (MD) is a highly contagious, lymphomatous disease of chickens induced by a herpesvirus, Marek’s disease virus (MDV) that is the cause of major annual losses to the poultry industry. MD pathogenesis involves multiple stages including an early cytolytic phase and latency, and transitions between these stages are governed by several host and environmental factors. The success of vaccination strategies has led to the increased virulence of MDV and selective breeding of naturally resistant chickens is seen as a viable alternative. While multiple gene expression studies have been performed in resistant and susceptible populations, little is known about the epigenetic effects of infection. Results: In this study, we investigated temporal chromatin signatures induced by MDV by analyzing early cytolytic and latent phases of infection in the bursa of Fabricius of MD-resistant and –susceptible birds. Major global variations in chromatin marks were observed at different stages of MD in the two lines. Differential H3K27me3 marks were associated with immune-related pathways, such as MAP kinase signaling, focal adhesion and neuroactive ligand receptor interaction, and suggested varying degrees of silencing in response to infection. Immune-related microRNAs, e.g. gga-miR-155 and gga-miR-10b, bore chromatin signatures, which suggested their contribution to MD-susceptibility. Finally, several members of the focal adhesion pathway, e.g. THBS4 and ITGA1, showed marked concordance between gene expression and chromatin marks indicating putative epigenetic regulation in response to MDV infection. Conclusions: Our comprehensive analysis of chromatin signatures, therefore, revealed further clues about the epigenetic effects of MDV infection although further studies are necessary to elucidate the functional implications of the observed variations in histone modifications. Total of 32 samples analyzed; 2 histone modifications - H3K4me3 and H3K27me3 x 2 chicken lines with varying resistance to MD - L63 and L72 x 2 time-points of disease progression - 5 and 10 days post infection x 2 conditions - infected and control x 2 biological replicates
2015-04-17 | E-GEOD-65961 | biostudies-arrayexpress
Project description:Marekâs disease (MD) is an economically significant disease in chickens caused by the highly oncogenic Marekâs disease virus (MDV). Understanding the genes and biological pathways that confer MD genetic resistance should lead towards the development of more disease resistant commercial poultry flocks or improved MD vaccines. MDV Meq, a bZIP transcription factor, is largely attributed for viral oncogenicity though only a few host target genes have been described, which has impeded our understanding of MDV-induced tumorigenesis. Given the importance of Meq in MDV-induced pathogenesis, we explored the role of Meq in genetic resistance to MDV. Using global transcriptome analysis to compare the host response between birds challenge with either wild type MDV or a recombinant lacking Meq, we identified a number of specific genes and pathways associated with either MD resistance. Integrating prior information from ChIP-seq, microarray analysis, and SNPs exhibiting allele-specific expression (ASE) in response to MDV infection from two inbred layer lines that differ greatly in MD genetic resistance, we were able to provide a evidence for 35 genes that SNPs within transcription factor binding sites can affect transcription factor binding and gene expression in an allele-specific manner. Transcript profiling of CEF's (a chicken embryo fibroblast cell line) from MD susceptible and resistant lines using Affymetrix chicken GeneChips
2016-07-01 | E-GEOD-48453 | biostudies-arrayexpress
Project description:Marek's disease virus (MDV) belongs to the alphaherpesviruses and is the causative agent of fatal T cell lymphomas in chickens. Aftermaths of MDV infections lead to substantial losses in poultry industry and there is evidence that MDV constantly evolves towards higher virulence. This study takes a detailed look at the very first step of the viral life cycle in the host: the infection of B cells. Recently, it has become possible to culture and infect primary chicken B cells ex vivo, enabling us to apply those cells to RNAseq analysis. Here, we provide novel insights into MDV gene expression profiles and post-transcriptional modifications of this important poultry pathogen in its primary target cells for lytic replication. Remarkably enough, we could detect a novel hypothetical MDV gene, identify multicistronic transcripts and previously unannotated splice forms. These findings lay the foundation for future research on MDV replication and pathogenesis and the developed bioinformatics pipeline can be easily transferred to other herpesviruses or large DNA viruses to identify unknown transcript isoforms and associated motifs.
2019-03-19 | E-MTAB-7772 | biostudies-arrayexpress
Project description:Background: Marek’s disease (MD) is a highly contagious, lymphomatous disease of chickens induced by a herpesvirus, Marek’s disease virus (MDV) that is the cause of major annual losses to the poultry industry. MD pathogenesis involves multiple stages including an early cytolytic phase and latency, and transitions between these stages are governed by several host and environmental factors. The success of vaccination strategies has led to the increased virulence of MDV and selective breeding of naturally resistant chickens is seen as a viable alternative. While multiple gene expression studies have been performed in resistant and susceptible populations, little is known about the epigenetic effects of infection. Results: In this study, we investigated temporal chromatin signatures induced by MDV by analyzing early cytolytic and latent phases of infection in the bursa of Fabricius of MD-resistant and –susceptible birds. Major global variations in chromatin marks were observed at different stages of MD in the two lines. Differential H3K27me3 marks were associated with immune-related pathways, such as MAP kinase signaling, focal adhesion and neuroactive ligand receptor interaction, and suggested varying degrees of silencing in response to infection. Immune-related microRNAs, e.g. gga-miR-155 and gga-miR-10b, bore chromatin signatures, which suggested their contribution to MD-susceptibility. Finally, several members of the focal adhesion pathway, e.g. THBS4 and ITGA1, showed marked concordance between gene expression and chromatin marks indicating putative epigenetic regulation in response to MDV infection. Conclusions: Our comprehensive analysis of chromatin signatures, therefore, revealed further clues about the epigenetic effects of MDV infection although further studies are necessary to elucidate the functional implications of the observed variations in histone modifications.
2015-04-17 | GSE65961 | GEO
Project description:To investigate specific miRNA expression profiles of Marek's disease virus (MDV)-infected samples, we performed deep sequencing for miRNAs in four small RNA libraries, including MDV-infected tumorous spleen, MD lymphoma from liver, and non-infected spleen and lymphocytes from controls. A total of 7.76x106, 6.36x106, 6.36x106, and 7.60x106 counts were obtained in four libraries, respectively. The sequences were blasted with chicken and MDV genomes and miRBase 16.0 to identify known and novel miRNAs. In total, 187 and 16 known mature miRNAs were identified in the chicken and MDV, respectively. Deep sequencing detected 942 novel chicken miRNA candidates, of which 646 were in tumorous spleen. These results indicate that MDV infection induced new host miRNA candidates and increased diversity of miRNAs. Of 942 miRNA candidates, 276 of 533 were verified by customized microarray, and 17 of them were further confirmed by qPCR.
2013-12-30 | GSE31349 | GEO