Ribosome profiling and RNA sequencing of Infectious Bronchitis Virus
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ABSTRACT:
PROVIDER: PRJEB32121 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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:Infectious bronchitis is a highly contagious respiratory disease of poultry caused by the coronavius infectious bronchitis virus (IBV). Until recently is was thought that coronavirus virions were composed of the structural proteins nucleocapsid, envelope, spike and membrane proteins, but investigations of TGEV and SARS-CoV have shown the proteome of coronavirus virions also includes viral non-structural and group specific proteins as well as host cell proteins. To study the proteome of IBV virions, virus was grown in embryonated chicken eggs and purified by sucrose gradient ultracentrifugation. Purified virus was analysed using sensitive gel-free proteomic techniques to determine the proteome of IBV. Analysis of three preparations of purified IBV yielded a list of 39 proteins commonly associated with the IBV virion. Three of these proteins were the viral structural proteins spike, membrane and nucleocapsid, but none of the viral non-strucutral or groups specific proteins could be identified. The other 35 proteins commonly associated to the IBV virion were all found to be host cell proteins. These proteins were classified into 12 categories using pantherdb (pantherdb.org). These proteins were involved in a diverse range of functions such as cytoskeletal proteins, nucleic acid binding proteins and chaperone proteins. Some of these proteins were unique to this study, whilst others were found to be orthologous to proteins identified in the SARS-CoV protein, and indeed some were also identified in association with virions from a number of other RNA and DNA viruses.
2016-02-15 | PXD002936 | Pride
Project description:Complete Genome analysis of Iranian IS-1494 like Avian Infectious Bronchitis virus
| PRJNA393073 | ENA
Project description:The S2 subunit of infectious bronchitis virus with flag tag was expressed in chick embryonic kidney cells, purified using flag antibody evolving immunoprecipitation, controls using igG antibody, and the resulting peptides or proteins were identified by protein profiling.
2024-04-24 | PXD041764 | JPOST Repository
Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of African green monkey (Vero E6) cells and Aedes albopictus (C6/36) cells infected with Zika Virus (ZIKV) strain PE243. Cells were harvested at 24 h post infection (p.i.) and Ribo-Seq and RNA-Seq libraries were prepared and deep sequenced.
2018-06-30 | E-MTAB-5418 | biostudies-arrayexpress
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 bursal disease virus Genome sequencing and assembly
| PRJNA488138 | ENA
Project description:To obtain the site-by-site methylation landscape of the infectious spleen and kidney necrosis virus (ISKNV) genome, whole-genome bisulfite sequencing (WGBS) was performed on an ISKNV strain from 3 duplicate samples.
2023-08-23 | GSE241500 | GEO