Mus musculus
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE59793MSV000078994
PROVIDER: PRJNA256196 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dynamic profiling of the protein life cycle in response to pathogens (protein)
| PRJNA256212 | ENA
Project description:Dynamic profiling of the protein life cycle in response to pathogens
| PRJNA256211 | ENA
Project description:Emerging and neglected pathogens pose challenges as their biology is frequently poorly understood, and genetic tools often do not exist to manipulate them. Organism agnostic sequencing technologies offer a promising approach to understand the molecular processes underlying these diseases. Here we apply dual RNA-seq to Orientia tsutsugamushi (Ot), the obligate intracellular causative agent of the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning, we investigated the transcriptional architecture of Ot, including operon structure and non-coding RNAs, and found evidence for wide-spread post-transcriptional antisense regulation. We compared the host response to two clinical isolates and identified distinct immune response networks that are up-regulated in response to each strain, leading to predictions of relative virulence which were confirmed in a mouse infection model. Thus, dual RNA-seq can reveal the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.
2020-06-05 | PXD017956 | JPOST Repository
Project description:Throughout HIV-1 replication cycle, a complex interplay of host-pathogen interactions takes place in the infected cell, leading to production of new virions. The virus modulates the host cellular machinery in order to support its life cycle, while controlling intracellular defense. We have investigated the dynamic host response to HIV-1 infection by systematically measuring transcriptome, proteome and phosphoproteome expression changes in infected and uninfected SupT1 CD4+ T cells at 5 time-points throughout the HIV-1 replication cycle. Genome-wide transcript levels were assessed by RNA-Seq, while protein and phosphoprotein relative abundances were obtained using SILAC mass spectrometry. By the means of a Gaussian mixed-effects model, we stratified host genes based on their gene expression temporal patterns at the three levels, showing how HIV may affect regulation of certain host genes. The results of the implemented integrative analysis of time-series omics data offers a catalogue of dynamic host response to HIV infection allowing a more comprehensive understanding of host-virus interactions. Furthermore, it facilitates identifying novel host factors potentially promoting or restricting HIV replication.
2018-12-31 | GSE100587 | GEO
Project description:Transcript Profiling of Arabidopsis Plant Life Cycle
| PRJNA87627 | ENA
Project description:<p>Mitochondrial metabolic remodeling is a hallmark of the Trypanosoma brucei digenetic life cycle since the insect stage utilizes the cost-effective oxidative phosphorylation to generate ATP, while bloodstream cells switch to less energetically efficient aerobic glycolysis. Due to difficulties in acquiring enough parasites from the tsetse fly vector for biochemical analysis, the dynamics of the parasite´s mitochondrial metabolic rewiring in the vector have remained obscure. Here, we took advantage of in vitro-induced differentiation to follow changes at the RNA, protein and metabolite levels. This multi-omics and cell-based profiling showed an immediate redirection of electron flow from the cytochrome mediated pathway to a mitochondrial alternative oxidase, an increase in proline consumption and its oxidation, elevated activity of complex II and certain TCA cycle enzymes, which led to mitochondrial inner membrane hyperpolarization and increased ROS levels in both mitochondrion and cytosol. Interestingly, these ROS molecules acted as signaling molecules driving developmental progression since exogenous expression of catalase, a ROS scavenger, halted the in vitro-induced cell differentiation. Our results provide insights into the mechanisms of the parasite´s mitochondrial rewiring and reinforce the emerging concept that mitochondria act as signaling organelles through release of ROS to drive cellular differentiation.</p><p><br></p><p><strong>Data availability:</strong></p><p><a href='https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE140796' rel='noopener noreferrer' target='_blank'>RNA-Seq</a></p><p>Proteomic data associated with this study are available in the PRIDE repository: accession number <a href='https://www.ebi.ac.uk/pride/archive/projects/PXD016370' rel='noopener noreferrer' target='_blank'>PXD016370</a>.</p>
2020-08-20 | MTBLS1390 | MetaboLights
Project description:RNA sequencing profiling showed differentially expressed genes implicated in categories such as DNA repair, type I interferon signaling and cell cycle. Moreover, a large amount of lncRNA were dysregulated after proton therapy, gemcitabine and olaparib. RNA sequencing profiling analysis presented dynamic alteration of transcriptome after chemoradiation and identified a classifier of gemcitabine response.
2021-02-21 | GSE165548 | GEO
Project description:Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons [IFN-I]. This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the pDC secretome in response to a physiologic stimulus has not been reported. We applied LC-MS/MS to catalogue the repertoire of proteins secreted by pDCs in response to challenge with live influenza H1N1. Additionally, using single-cell RNA-seq [scRNA-seq], we perform multidimensional analyses of pDC transcriptional diversification following stimulation. Our data reveal an abundance of protein species released by pDCs in addition to IFN-I, and evidence highly specialized roles within the pDC population ranging from dedicated cytokine super-producers to cells with APC-like functions. Moreover, dynamic expression of transcription factors and surface markers characterize activated pDC fates.
2021-11-12 | MSV000088375 | MassIVE
Project description:The parasitic flagellate Trypanosoma vivax is a cause of animal trypanosomiasis across Africa and South America. The parasite has a digenetic life cycle, passing between mammalian hosts and insect vectors, and a series of developmental forms adapted to each life cycle stage. Transcriptomic and proteomic studies of the related parasites T. brucei and T. congolense have shown how gene expression is regulated during their development. New methods for in vitro culture of the T. vivax insect stages have allowed us to describe global gene expression throughout the complete T. vivax life cycle for the first time. We combined transcriptomic and proteomic analysis of each life stage using RNA-seq and mass spectrometry respectively, to identify genes with patterns of preferential transcription or expression. While T. vivax is similar to related species in several ways, (e.g. developmental regulation of energy metabolism, restricted expression of a dominant variant antigen, and expression of ‘Fam50’ proteins in the insect mouthparts), we identify significant differences in gene expression affecting metabolism in the fly and a suite of T. vivax-specific genes with predicted cell-surface expression that are preferentially expressed in the mammal (‘Fam29, 30’) or the vector (‘Fam34, 35, 43’). Thus, T. vivax differs significantly from other African trypanosomes in the developmentally-regulated proteins it expresses on its cell surface and thus, in the structure of the host-parasite interface. These unique features may yet explain the species differences in life cycle and could, in the shape of bloodstream-stage proteins that do not undergo antigenic variation, provide targets for therapy.
2015-07-20 | PXD001617 | Pride