Pseudorabies virus transcriptome sequencing
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR908011.fastq.gz | Fastqsanger.gz | |||
| ERR908011_1.fastq.gz | Fastqsanger.gz | |||
| ERR908011_2.fastq.gz | Fastqsanger.gz | |||
| ERR908012.fastq.gz | Fastqsanger.gz |
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Project description:RNA isolated from draining tracheobronchial lymph nodes (TBLN) from 5-week old pigs, either clinically infected with a feral isolate of Pseudorabies virus or uninfected were interrogated using Illumina Digital Gene Expression Tag Profiling. Over 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences collected from TBLN at time points 1, 3, 6 and 14 days post-infection (dpi)
2015-10-30 | GSE74473 | GEO
Project description:RNA isolated from draining tracheobronchial lymph nodes (TBLN) from 5-week old pigs, either clinically infected with a feral isolate of Pseudorabies virus or uninfected were interrogated using Illumina Digital Gene Expression Tag Profiling. Over 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences collected from TBLN at time points 1, 3, 6 and 14 days post-infection (dpi) RNA isolated from draining tracheobronchial lymph nodes (TBLN) from 5-week old pigs (% per group pooled), either clinically infected with feral isolate FS268 of Pseudorabies virus or uninfected at 1, 3, 6, and 14 days post inoculation. Over 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences.
2015-10-30 | E-GEOD-74473 | biostudies-arrayexpress
Project description:Six piglets (age 2-4 days) suffering from pseudorabies virus were identified during at outbreak at a commercial farm. RNA was extracted from lung (n=4) and brain (n=6) of the infected pigs, and compared to lung/brain RNA from a control pool of three uninfected piglets. Expression profiling used a human oligonucleotide geneset.
2009-10-02 | E-MEXP-2376 | biostudies-arrayexpress
Project description:Pseudorabies, an acute infectious disease caused by pseudorabies virus (PRV), has caused enormous economic losses to the breeding industry in many countries worldwide. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) may play important roles in the antiviral responses. However, little is known about the identification and functions of swine lncRNAs in cellular antiviral responses against PRV II. In this study, we detected the expression profiles of host lncRNAs and mRNAs from PRV-DX, a wild-type (WT) strain of PRV II, and its attenuated gE-TK- PRV-DX infected cells by high-throughput RNA sequencing. Finally, we identified differentially expressed (DE) 664 lncRNAs and DE 7,199 mRNAs from PRV-DX infected cells, and 654 DE lncRNAs and DE 7,149 mRNAs from gE-TK- PRV-DX infected cells when compared to MOCK infected cells, respectively, especially including 469 common DE lncRNAs and 5836 DE mRNAs. Besides 276 DE lncRNAs and 2,272 DE mRNAs between PRV-DX and gE-TK- PRV-DX infected cells were identified. The potential functions of the significant DE lncRNAs were involved in interleukin secretion, axon extension and metabolic process based on the Gene ontology and Kyoto Encyclopedia of Genes and Genomes databases. Taken together, results highlighted the potentials of lncRNA as targets for antiviral therapy and enriched the current knowledge of the mechanisms underlying the interaction between PRV II and its host cells.
2022-07-11 | GSE134133 | GEO
Project description:Pseudorabies virus (PRV), the etiological agent of Aujeszky’s disease, is a swine pathogen of the alphaherpesvirinae subfamily resulting in devastating neurological and respiratory disorders in piglets, or abortion in pregnant sows.Here, we performed isobaric tags for relative and absolute quantitation (iTRAQ) quantitative phosphoproteomics on PRV-infected PK-15 cells, which identified 5723 phospho-peptides, corresponding to 2180 proteins, including 810 proteins showing significant changes in phosphorylation level during early PRV infection.
2022-10-13 | PXD014685 | Pride
Project description:BackgroundPseudorabies virus is a widely-studied model organism of the Herpesviridae family, with a compact genome arrangement of 72 known coding sequences. In order to obtain an up-to-date genetic map of the virus, a combination of RNA-sequencing approaches were applied, as recent advancements in high-throughput sequencing methods have provided a wealth of information on novel RNA species and transcript isoforms, revealing additional layers of transcriptome complexity in several viral species.ResultsThe total RNA content and polyadenylation landscape of pseudorabies virus were characterized for the first time at high coverage by Illumina high-throughput sequencing of cDNA samples collected during the lytic infectious cycle. As anticipated, nearly all of the viral genome was transcribed, with the exception of loci in the large internal and terminal repeats, and several small intergenic repetitive sequences. Our findings included a small novel polyadenylated non-coding RNA near an origin of replication, and the single-base resolution mapping of 3' UTRs across the viral genome. Alternative polyadenylation sites were found in a number of genes and a novel alternative splice site was characterized in the ep0 gene, while previously known splicing events were confirmed, yielding no alternative splice isoforms. Additionally, we detected the active polyadenylation of transcripts earlier believed to be transcribed as part of polycistronic RNAs.ConclusionTo the best of our knowledge, the present work has furnished the highest-resolution transcriptome map of an alphaherpesvirus to date, and reveals further complexities of viral gene expression, with the identification of novel transcript boundaries, alternative splicing of the key transactivator EP0, and a highly abundant, novel non-coding RNA near the lytic replication origin. These advances provide a detailed genetic map of PRV for future research.
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Project description:Porcine PARP11 is essential for the proliferation of pseudorabies Virus
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Project description:<p>Pseudorabies virus infection causes intestinal flora disorder in animals, leading to diarrhea. To explore the effect of inactivated pseudorabies vaccine immunization on pseudorabies virus infection, this study sequenced the serum metabolome and intestinal microbiota of Hu sheep, analyzed their differential expression and conducted a combined analysis. The results showed that all the Hu sheep in the vaccine immunization group survived, while those in the non-immunization group died. The expressions of quercetin, 3, 7-dimethylquercetin, 5-Methoxyindoleacetate, L-methionine, L-glutamic acid, thymine, adenine and 20-HETE were upregulated in the serum of the vaccine immunization group (P<0.05). The expressions of amifostine, hemialdehyde succinate and trehalose were down-regulated (P<0.05). The microbiota structure and abundance in the vaccine immunization group changed significantly, and the beneficial bacteria Christensenellaceae_R-7_group, Bifidobacterium, Solibacillus, and Rikenellaceae_RC9_gut_group increased. The results of the combined omics analysis showed that the changes of metabolites such as quercetin, 3, 7-dimethylquercetin, 5-Methoxyindoleacetate and adenine were positively correlated with the abundance changes of Rikenellaceae_RC9_gut_group (P<0.05); L-methionine and 20-HETE were positively correlated with adenine and Solibacillus (P<0.05); Succinate semialdehyde was significantly negatively correlated with Rikenellaceae_RC9_gut_group. The above results indicate that after inactivated pseudorabies vaccine immunization of Hu sheep, it affects metabolites (quercetin, 3, 7-dimethylquercetin, 5-Methoxyindoleacetate adenine, L-methionine and 20-HETE) by maintaining beneficial intestinal bacteria (Rikenella aceae_RC9_group and Solibacillus). Metabolites jointly regulate the generation of inflammatory mediators, influence the function of immune cells and participate in the regulation of oxidative stress, thereby exerting an immune protective effect. This study provides an important theoretical basis for a deeper understanding of the immune protection mechanism of inactivated pseudorabies vaccine.</p>
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Project description:<p>Pseudorabies virus infection causes intestinal flora disorder in animals, leading to diarrhea. To explore the effect of inactivated pseudorabies vaccine immunization on pseudorabies virus infection, this study sequenced the serum metabolome and intestinal microbiota of Hu sheep, analyzed their differential expression and conducted a combined analysis. The results showed that all the Hu sheep in the vaccine immunization group survived, while those in the non-immunization group died. The expressions of quercetin, 3, 7-dimethylquercetin, 5-Methoxyindoleacetate, L-methionine, L-glutamic acid, thymine, adenine and 20-HETE were upregulated in the serum of the vaccine immunization group (P<0.05). The expressions of amifostine, hemialdehyde succinate and trehalose were down-regulated (P<0.05). The microbiota structure and abundance in the vaccine immunization group changed significantly, and the beneficial bacteria Christensenellaceae_R-7_group, Bifidobacterium, Solibacillus, and Rikenellaceae_RC9_gut_group increased. The results of the combined omics analysis showed that the changes of metabolites such as quercetin, 3, 7-dimethylquercetin, 5-Methoxyindoleacetate and adenine were positively correlated with the abundance changes of Rikenellaceae_RC9_gut_group (P<0.05); L-methionine and 20-HETE were positively correlated with adenine and Solibacillus (P<0.05); Succinate semialdehyde was significantly negatively correlated with Rikenellaceae_RC9_gut_group. The above results indicate that after inactivated pseudorabies vaccine immunization of Hu sheep, it affects metabolites (quercetin, 3, 7-dimethylquercetin, 5-Methoxyindoleacetate adenine, L-methionine and 20-HETE) by maintaining beneficial intestinal bacteria (Rikenella aceae_RC9_group and Solibacillus). Metabolites jointly regulate the generation of inflammatory mediators, influence the function of immune cells and participate in the regulation of oxidative stress, thereby exerting an immune protective effect. This study provides an important theoretical basis for a deeper understanding of the immune protection mechanism of inactivated pseudorabies vaccine.</p>
2025-09-03 | MTBLS12933 | MetaboLights
Project description:In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we carried out a systematic analysis on the pseudorabies virus transcriptome by combining our current data obtained by using Pacific Biosciences Sequel and Oxford Nanopore Technologies MinION sequencing with our earlier data generated by other LRS and short-read sequencing techniques. As a result, we identified a number of novel genes, transcripts, and transcript isoforms, including splice and length variants, and also confirmed earlier annotated RNA molecules. One of the major findings of this study is the discovery of a large number of 5'-truncations of larger putative mRNAs being 3'-co-terminal with canonical mRNAs of PRV. A large fraction of these putative RNAs contain in-frame ATGs, which might initiate translation of N-terminally truncated polypeptides. Our analyses indicate that CTO-S, a replication origin-associated RNA molecule is expressed at an extremely high level. This study demonstrates that the PRV transcriptome is much more complex than previously appreciated.
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