Virus sp. strain:provirus | isolate:host
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1219074 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human immunodeficiency virus (HIV) infection is a chronic condition, where viral DNA integrates into the genome. The fate of the provirus determines the infection course. Latently infected cells form a persistent, heterogeneous reservoir. The reservoir that reinstates an active infection comprises cells with intact provirus that can be reactivated. We confirmed that latent cells from patients exhibited active transcription throughout the provirus. To find transcriptional determinants, we characterized the establishment and maintenance of latency during proviral chromatin maturation in primary CD4+ T-cells for four months after HIV infection. As heterochromatin (marked with H3K9me3 or H3K27me3) gradually stabilized, the provirus became less accessible and lost activation potential. In a subset of infected cells, active marks (i.e., H3K27ac) remained detectable, even after prolonged proviral silencing. After T-cell activation, the proviral activation occurred uniquely in cells with H3K27ac-marked proviruses. Our observations suggested that, after transient proviral activation, cells were actively returned to latency.
2019-12-16 | GSE121055 | GEO
Project description:description Blastocystis sp. is a highly prevalent anaerobic eukaryotic parasite of humans and animals. The genome of several representatives has been sequenced revealing specific traits such as an intriguing 3’-end processing of primary transcripts. We have acquired a first high-throughput proteomics dataset on the difficult to cultivate ST4 isolate WR1 and detected 2,761 proteins. We evidenced for the first time by proteogenomics a functional termination codon derived from transcript polyadenylation for seven different key cellular components.
2017-09-11 | PXD006588 | Pride
Project description:Chikungunya virus (CHIKV) infection is characterized by alterations in gene expression profile on host cells that consequently lead to an immune response. Here, we used RNA sequencing to analyze the mRNA expression profile in human monocyte-derived macrophages (MDMs) infected with a Colombian clinical isolate of CHIKV at 6 and 24 hpi. analyze the mRNA expression profile in the human monocyte-derived macrophages infected at 6 and 24 hrs with a Colombian clinical isolate of Chikungunya virus.
2022-01-19 | GSE193977 | GEO
Project description:In rainbow trout, type A spermatogonia can be split into SP cells and non-SP cells by the ability to exclude Hoechst 33342 dye (H33342). The H33342 fluorescence of SP cells are lower than that of non-SP cells, after H33342 staining. To investigate whether SP cells were transcriptomically distinct from non-SP cells, we compared the transcriptome of these cells. We used fluorescence-activated cell sorting (FACS) to isolate SP cells and non-SP cells from the type A spermatogonia in rainbow trout.
2013-08-06 | GSE49565 | GEO
Project description:Haloferax volcanii harbours four putative proviruses: Halfvol1, Halfvol2, Halfvol3 and Halfvol4. In this study we successfully deleted all four provirus genomes, demonstrating, that they are not essential. Transcriptome comparison between this strain (∆Halfvol1-4) and a wild type strain reveals an increase in archaella and chemotaxis gene expression, resulting in higher swarming motility in ∆Halfvol1-4. Furthermore, ∆Halfvol1-4 cells show an elongated cell shape and a higher resistance to H2O2 stress compared to the wild type. RNA-seq also revealed down-regulation of CRISPR arrays in the provirus-free strain. Circularised genomes of Halfvol1, Halfvol2 and Halfvol3 were found in the culture supernatant. This confirms excision of the proviruses from the chromosome, which seems to happen more efficiently at low temperature (30°C). Electron microscopy revealed potential viral particles in the supernatant, and mass spectrometry analysis confirmed the presence of structural viral proteins of Halfvol1 and Halfvol3 in the isolated virus sample. These observations suggest that these proviruses are active and cause a chronic infection in Hfx. volcanii.
2025-05-26 | PXD058393 | Pride
Project description:Bacillus sp. (in: firmicutes) isolate:host,fish Genome sequencing
| PRJNA1063019 | ENA
Project description:immunoprecipitation-mass spectrometry related to rice stripe virus SP
2025-05-07 | PXD063713 |
Project description:Plum pox virus (PPV, family Potyviridae) is one of the most important viral pathogens of Prunus spp. causing considerable damage to stone-fruit industry worldwide each year. Among the PPV strains identified so far, only PPV-C and PPV-CR are able to infect cherries under natural conditions. Herein, we evaluated the impact of strains differing by the pathogenic potential on herbaceous host Nicotiana benthamiana. At first glance, a faster accumulation of PPV capsid protein was noticed by semi-quantitative DAS-ELISA on tobacco leaves infected by PPV-CR (the RU-30sc isolate) in contrast to PPV-C (BY-101 isolate). This result was correlated perfectly with observed phenotypic symptoms. To assess the host response to infection more deeply, a comprehensive proteomic profiling was performed using reverse phase UHPLC followed by label-free mass spectrometry quantification. Thirty-one unique plant proteins were identified as significantly altered due to the infection. Precise evaluation of particular amount shifts of identified proteins in relation to infection has revealed that the aggressive PPV-CR isolate has a stronger influence on the abundance of photosynthesis-related proteins, mainly from Calvin cycle, as the mild PPV-C. This observation was accompanied by a significant reduction of photosynthetic pigments extracted from the leaves of PPV-CR infected plants. Shifts in the abundance of remaining identified proteins, indicates activation of repair mechanism, stimulation of photosynthetic capacity, and modifications in amino acid and carbohydrate metabolism to affect plant growth and initiate energy formation via gluconeogenesis. Furthermore, we speculate that accumulation of H2O2, in PPV-CR infected leaves may activate glutathione synthesis, which plays a crucial role in further plant defense and development.
2018-08-13 | PXD010018 | Pride
Project description:Florenciella sp. virus SA2 isolate genome sequencing
| PRJNA1169927 | ENA