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E-MTAB-5947

ABSTRACT: Transcription profiling by array of differential gene expression in chicken primary B cells infected ex vivo with attenuated and very virulent strains of infectious bursal disease virus (IBDV)

PROVIDER: E-MTAB-5947 | ExpressionAtlas | 2017-08-16

REPOSITORIES: ExpressionAtlas

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Microarray of MDV infected cultured chicken bursa cells

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

Transcription profiling by array of differential gene expression in chicken primary B cells infected ex vivo with attenuated and very virulent strains of infectious bursal disease virus (IBDV)

Project description:Infectious bursal disease virus (IBDV) belongs to the family Birnaviridae and is economically important to the poultry industry worldwide. IBDV infects B cells in the bursa of Fabricius (BF), which can cause severe immunosuppression and mortality in young chickens. Earlier studies have shown that strains of IBDV lose their virulence potential after serial passage in non-B lymphoid cells, for reasons that are poorly understood. This study aimed to investigate the gene expression profiles of one cell-culture adapted attenuated IBDV strain (D78) and one very virulent IBDV strain (UK661) in chicken primary B cells cultured ex vivo from the bursa of Fabricius. The viruses were studied in B cells over 48h and their gene expression was initially evaluated with qPCR. The mRNA was isolated from the cells at 18 hours post-infection and screened with Affymetrix microarrays in triplicate. The study included mock controls which were conducted in triplicate.

2017-11-01 | E-MTAB-5947 | biostudies-arrayexpress

The severity of infectious bursal disease in White Leghorn inbred chicken lines is associated with greater bursal inflammation in vivo and more rapid induction of pro-inflammatory responses following ex vivo stimulation of primary bursal cells.

Project description:Transcriptomics analysis reveals that severity of infectious bursal disease in White Leghorn inbred chicken lines is associated with greater bursal inflammation in vivo and more rapid induction of pro-inflammatory responses following ex vivo stimulation of primary bursal cells. In order to better understand differences in the outcome of infectious bursal disease virus (IBDV) infection, we inoculated very virulent (vv) IBDV into White Leghorn chickens from inbred line W that previously had over 24% mortality, and three inbred lines (15I, C.B4 and O) that previously had 0% mortality. Within each experimental group, some individuals experienced more severe disease than others but line 15I birds experienced milder disease based on average clinical scores, percentage of birds with gross pathology, average bursal lesion scores and average peak bursal virus titre. RNA-Seq analysis revealed that more severe disease was associated with a significant up-regulation of pathways involved in inflammation, cytoskeletal regulation by Rho GTPase, nicotinic acetylcholine receptor signaling, and Wnt signaling in the bursa. Primary bursal cells cultured from line W birds and stimulated ex vivo with LPS had a more rapid up-regulation of pro-inflammatory gene expression than cells from line 15I birds, and line W birds had a significantly greater percentage of KUL01+ macrophage cells in the BF than line 15I birds. We hypothesize that a more rapid induction of pro-inflammatory cytokine responses in line W birds causes excessive inflammation and clinical disease following IBDV infection compared to line 15I, and we suggest that pro-inflammatory pathways could be targeted to engineer more disease resistant birds in the future

2021-06-02 | GSE166026 | GEO

Transcriptome analysis in primary cell models of HIV latency and cells from HIV-infected ART-suppressed individuals

Project description:Comparison of total RNA-seq data from ex vivo unstimulated and stimulated (with anti-CD3/CD28) cells from two primary cell models of HIV latency (resting-cell and wild-type virus models) and peripheral CD4+ T cells from HIV-infected ART-suppressed individuals (ex vivo cells). Two donors were analyzed per model.

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The Transcriptional Landscape of Marek’s Disease Virus in Primary Chicken B Cells Reveals Novel Splice Variants and Genes

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

Expression data from low- and high-pathogenicity avian influenza-infected chicken and duck cells

Project description:While infection of chickens with highly pathogenic avian influenza (HPAI) H5N1 subtypes often leads to complete mortality within 24 to 48 h, infection of ducks in contrast causes mild or no clinical signs. Rapid onsets of fatal disease in chickens, but with no evidence of severe clinical symptoms in ducks, suggest underlying differences in their innate immune mechanisms. To understand the molecular basis for such difference, chicken and duck primary lung cells, infected with a low-pathogenicity avian influenza (LPAI) and two HPAI H5N1 viruses, were subjected to RNA expression profiling using Affymetrix Chicken GeneChip arrays. We used microarrays to analyze the gene expression profiles of primary chicken and duck lung cells infected with H2N3 LPAI and two H5N1 influenza virus subtypes to understand the molecular basis of host susceptibility and resistance. We have identified a set of key genes and pathways that could play an important role in mediating innate host resistance to avian influenza in chickens and ducks. 24 hours following infection, total RNA from cells was extracted. Replicate RNA samples from each of the virus-infected (H2N3, H5N1 50-92, or H5N1 ty-Ty) or mock-infected chicken and duck cells (4 treatment groups for each species) were used for microarray analysis. Each of the RNA samples was hybridized to one GeneChipM-BM-. Chicken Genome Array (Affymetrix), and a total of 16 array chips were used.

2014-12-04 | E-GEOD-33389 | biostudies-arrayexpress

Lung proteome analysis of highly pathogenic avian influenza virus (H5N1) infection progression in chicken

Project description:This study is planned to characterize the proteome profile of HPAI H5N1 virus infected chicken lung tissues to identify the molecular pathogenesis and proteomic determinant associate with disease progression in susceptible host.

2022-03-02 | PXD010358 | Pride

Chicken Spleen Tissues: MDV-infected vs non-infected in inbred lines 63, 72 & RCSM

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

Ribosome profiling and RNA sequencing of Infectious Bronchitis Virus

Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of chicken (Gallus gallus) cells infected with Infectious Bronchitis Virus (IBV) strains Beaudette and M41.

2019-06-18 | E-MTAB-7849 | biostudies-arrayexpress

HiSeq analysis of human gene expression profile following infection with highly pathogenic avian influenza A virus (H5N1; A/Chicken/Vietnam/0008/04)

Project description:Current prophylactic and therapeutic strategies targeting human influenza viruses include vaccines and antivirals. Given variable rates of vaccine efficacy and antiviral resistance, alternative strategies are urgently required to improve disease outcomes. Here we describe the use of HiSeq deep sequencing to analyze host gene expression in primary human alveolar epithelial type II (ATII) cells infected with highly pathogenic avian influenza H5N1 virus. We employed primary human ATII cells isolated from normal human lung tissue donated by patients that underwent lung resection. Human host gene expression following HPAI H5N1 virus (A/Chicken/Vietnam/0008/04) infection of primary ATII cells was analyzed using Illumina HiSeq deep sequencing.

2018-10-09 | GSE119767 | GEO

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