Dataset's files
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| SRR25023888_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Avian infectious bronchitis virus (IBV) was an major respiratory disease-causing agents that lead to significant losses in birds. Dendritic cells (DCs), an major antigen-presenting cells, influence viruses pathogenicity as well as host immune response. Expression of host non-coding mRNA changes markedly during infectious bronchitis virus (IBV) infection of avian, but their role in regulating host immune function to defend IBV infection has not been explored. Here, microarray, including mRNAs, miRNAs and lncRNAs, were analysed to better understand the interaction between IBV and avian DCs. Results: Firstly, we found that IBV infection can effectively induce avian DCs to become mature. Interestingly, inactivated IBV possess high ability in inducing DC maturation and activating lymphocytes than that in actived IBV stimulated group. Then, result identified that IBV infection induced 1093 upregulated and 845 downregulated mRNAs in avian DCs. Analysis of Gene Ontology suggested that celluar macromolecule and protein location (GO-BP), as well as transcription factor binding (GO-MF) were abundance in IBV infected group. Whilst, pathway analyses suggested that oxidative phosphorylation and T cell receptor signalling pathways might activated in IBV group. Moreover, microRNA (miRNA) and long non-coding RNA (lncRNA) alterations in IBV-stimulated avian DCs were observed. A total of 19 significantly altered (7 up and 12 down) miRNAs and 101 (75 up and 26 down) lncRNAs were identified in IBV-stimulated DCs. Furtherly insight analyses not only gain that regulation of actin cytoskeleton and MAPK signal pathway were contributed to IBV stimulated miRNAs target genes, but also build an regulatory networks based on co-expressed lncRNA and mRNA. Finally, our study identified 2 TF-miRNA (CEBPA-miR1772 and CEBPA-miR21), which we based on to constructed 53 transcription factor (TF)–miRNA–mRNA interactions involving 1 TF, 2 miRNAs, and 53 mRNAs in IBV-stimulated avian DCs.
2017-12-01 | GSE100802 | GEO
Project description:Infectious bronchitis virus (IBV), is a coronavirus which infects chickens (Gallus gallus), and is one of the foremost causes of economic loss within the poultry industry, affecting the performance of both meat-type and egg-laying birds. The virus replicates not only in the epithelium of upper and lower respiratory tract tissues, but also in many tissues along the alimentary tract and elsewhere e.g. kidney, oviduct and testes. It can be detected in both respiratory and faecal material. There is increasing evidence that IBV can infect species of bird other than the chicken. Interestingly breeds of chicken vary with respect to the severity of infection with IBV, which may be related to the immune response (Cavanagh, 2006). Here we examine differential expression of genes in the trachea of susceptible and resistant birds, in order to identify genes which may be involved in resistance to IBV.
2015-07-31 | E-TABM-1128 | biostudies-arrayexpress
Project description:Influenza B virus (IBV) is considered a major respiratory pathogen responsible for seasonal respiratory disease in humans, particularly severe in children and the elderly. Seasonal influenza vaccination is considered the most efficient strategy to prevent and control IBV infections. Live attenuated influenza virus vaccines (LAIVs) are thought to induce both humoral and cellular immune responses by mimicking a natural infection, but their effectiveness have recently come into question. Thus, the opportunity exists to find alternative approaches to improve overall influenza vaccine effectiveness. Two alternative IBV backbones were developed with re-arranged genomes, re-arranged M (FluB-RAM) and a re-arranged NS (FluB-RANS). Both re-arranged viruses showed temperature sensitivity in vitro compared to the WT type B/Bris strain, were genetically stable over multiple passages in embryonated chicken eggs and were attenuated in vivo in mice. In a prime-boost regime in naïve mice, both re-arranged viruses induced antibodies against HA with hemagglutination inhibition titers considered of protective value. In addition, antibodies against NA and NP were readily detected with potential protective value. Upon lethal IBV challenge, mice previously vaccinated with either FluB-RAM or FluB-RANS were completely protected against clinical disease and mortality. In conclusion, genome re-arrangement renders efficacious LAIV candidates to protect mice against IBV.
2021-07-23 | GSE180642 | GEO
Project description:Avian infectious bronchitis virus (IBV) infection is a major chicken viral respiratory disease that causes significant economic losses to the poultry industry worldwide. The local mucosal immune response plays a vital role against the infection of this respiratory virus. Previous studies have indicated that a variety of innate immunity and a Th1 based adaptive immunity are activated in the host’s early defense (3 days post inoculation, dpi) against IBV invasion and they are responsible for the rapid clearance of virus from the local infection. In the present study, we propose to use IBV as a model system to uncover the molecular mechanism of mucosal immunity development by characterizing the kinetics of the local gene transcription profiles in trachea tissues after administration with an attenuated IBV strain (IBV-Mass). More specifically, immune-related gene transcription profiles in trachea at 1, 3, 5, 8, 12 and 21 days after the primary immunization and at 1 and 2 days after a second immunization were monitored using chicken 13K cDNA Microarray. Keywords: time course, cDNA 13k chicken array from FHCRC, IBV-chicken model
2006-11-03 | GSE6198 | GEO
Project description:Prostate cancer cell lines grow in full serum under standard conditions were profiled on Agilent-014698 Human Genome CGH Microarray 105A. Digestion, labeling, hybridization and data analysis of genomic DNA were performed according to the Agilent Technologies (Santa Clara, CA) protocol version 6.0 for 105 K arrays.
2011-02-01 | GSE26447 | GEO
Project description:EBPR full cycle of Ca. Accumulibacter SCUT-4 (0,20,40,80,116,152min))
| PXD056138 |
Project description:ChIP-seq experiment of 14 human lymphoblastoid cell line samples from the 1000 Genomes sample set (http://www.1000genomes.org/). Dataset includes two parent-daughter trios (CEU and YRI populations) and additional eight unrelated individuals (CEU population). This accession contains raw and mapped ChIP-seq read data, other assays in this study are available under accession E-MTAB-1883 (RNA-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1883) and E-MTAB-1885 (GRO-seq, https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1885/).
2013-10-17 | E-MTAB-1884 | biostudies-arrayexpress
Project description:Human SARS-CoV-2 and avian IBV are highly contagious and deadly coronaviruses causing devastating respiratory diseases in human and chicken, respectively. Lacking effective therapies exacerbates the disease associated with SARS-CoV-2 and IBV infections. Thus, novel therapeutic agents are in demand for controlling viral transmission and disease progression. Mesenchymal stem cells secreted factors (secretome) proven to be safe and highly efficient alternative to stem cells in mesenchymal stem cell-based therapy (MSCT). The most favorable advantage of secretome is the bypass of the side effects of MSCT that include but not limited to tumorigenesis, immune rejection, and infection. In this study, we aimed to investigate the antiviral activities of human Wharton’s jelly mesenchymal stem cells secretome against SARS-CoV-2 and IBV infection. The half-maximal inhibitory concentrations (IC50), and cytotoxic concentration (CC50) values of hWJ-MSC secretome (hWJ-MSC-S) were determined in Vero-E6 cells. Virucidal, anti-adsorption, and anti-replication mechanisms of hWJ-MSC-S against SARS-CoV-2 and IBV infection were evaluated in vitro. In Ovo anti-IBV activity of hWJ-MSC-S was estimated using Specific pathogen-free (SPF) embryonated chicken eggs (ECEs). The antiviral efficacy of hWJ-MSC-S was determined in terms of reduction in viral infection. Protein composition of hWJ-MSC-S was analyzed by mass spectrometry analysis, and gene ontology of secretome proteins was evaluated. Our data showed hWJ-MSC-S to significantly inhibits infection of human SARS-CoV-2 and avian IBV with very low cytotoxicity and embryotoxicity profile. CC50 value of hWJ-MSC-S in Vero-E6 was 39200 µg/ml. IC50, SI values of hWJ-MSC secretome against SARS-CoV-2 were 166.6 µg/ml, and 235.29, respectively. Similarly, IC50, SI values of hWJ-MSC-S against IBV were 439.9 µg/ml, and 89.11, respectively. hWJ-MSC-S reduced PFU/ml of SARS-CoV-2 and IBV by > 90%. Antiviral mechanistic studies demonstrated that hWJ-MSC-S had >95% and >90% virucidal effects on SARS-CoV-2 and IBV infections, respectively. The anti-replication effect was approximately 87.33% against SARS-CoV-2 infection, and >90% against IBV infection. In ovo model, hWJ-MSC-S significantly inhibited IBV infection. At a concentration of 1000 µg/ml, hWJ-MSC-S reduced IBV titre from 763000 ± 32638 to 38.333 ± 6.0093 EID50/ml (>99% inhibition). Similarly, hWJ-MSC-S reduced IBV titer from 763000 ± 32638 to 1896 ± 926.1 EID50/ml (>97% inhibition) at a concentration of 500 µg/ml. In addition, 250 µg/ml concentration of hWJ-MSC-S reduce IBV titer from 763000 ± 32638 to 20380 ± 2885 EID50/ml (>96% inhibition). LC/MS-MS analysis revealed that biological processes of hWJ-MSC-S proteins were mostly related to Immunomodulatory effect. Collectively, our results not only uncovered the antiviral potency of hWJ-MSC-S against SARS-CoV-2 and IBV, but also described the mechanism by which hWJ-MSC-S inhibit viral infection. These findings could be utilized in future pre-clinical and clinical studies to develop an effective therapeutic against human COVID-19 and avian IB respiratory diseases using hWJ-MSC-S.
2022-06-09 | PXD030966 | Pride
Project description:To understand the mechanistic basis of local innate and adaptive immunity against infectious bronchitis virus (IBV) at the molecular level, we examined the gene transcription profile of tracheal epithelial layers at 3 days after infection of chickens with an attenuated IBV-Massachusetts strain. Keywords: Disease State Analysis, Early mucosal immune response, FHCRC 13k chicken array
2006-11-03 | GSE6211 | GEO
Project description:Influenza B virus (IBV), though often overshadowed by influenza A viruses (IAVs), remains a significant global public health concern, particularly during seasons when it predominates. However, the molecular mechanisms underlying IBV pathogenicity remain largely unknown. In this study, we analyzed polymerase polymorphisms in an IBV isolated from a single patient’s oropharyngeal swab and identified two plaque colonies with distinct replication and pathogenicity phenotypes, associated with the PB2:N460S and NP:I163T substitutions. Using reverse genetics, we generated recombinant IBV mutants to evaluate the impact of these substitutions. The results showed that while neither mutation alone significantly affected viral replication or pathogenicity, their combination markedly enhanced both. Transcriptomic analysis of infected lung tissues revealed heightened immune activation, including upregulation of antiviral and immune-related genes, contributing to excessive inflammation and disease severity. Mechanistically, both substitutions increased protein expression and strengthened PB2-NP interaction, but only together did they enhance polymerase activity. Structural modeling suggested that PB2:460 is positioned at the PB2-NP interface, whereas NP:163 is not, indicating an indirect functional interplay. These findings provide new insights into the molecular determinants of IBV pathogenesis, highlighting the synergistic effect of PB2:N460S and NP:I163T in enhancing viral fitness and exacerbating disease outcomes.
2025-08-21 | GSE289500 | GEO