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MetabolomicsMicrobiomics combined metabolomics reveals Akkermansia modulating chicken gut microenvironment to protect from gamma coronavirus infection

In this study, we comprehensively investigated the influence of gut microbiota on gamma coronavirus replication in chickens. Using multi-omics approaches, we systematically examined microbial, viral and metabolic differences among adult chickens, young chickens and young chickens subjected to fec...

2025-08-17 | MTBLS12310 | MetaboLights
ProteomicsPRM quantification of MCS proteins and viral proteins in HCMV virus microenvironment
The control of host processes which influence cell-cell communication is central to determining the outcome of a virus infection in tissue. Despite this, it remains unclear how cells either in close or distant proximity to an infected cell differentially respond to the primary infection. We establis...
ORGANISM(S): Homo Sapiens Human Betaherpesvirus 5 
2023-05-22 | PXD038466 | panorama
MetabolomicsIntegrated Multi-Omics Analysis Reveals the Impact of Vaginal Microbiota on the Microenvironment During Cervical Precancerous Progression

In this study, 172 HPV-positive patients were enrolled, of which 103 were diagnosed with low-grade squamous intraepithelial lesion (LSIL) and 69 with high-grade squamous intraepithelial lesion (HSIL). Vaginal secretions from 90 (60 with HSIL and 30 with LSIL) of these patients were collected in 8...

2025-09-19 | MTBLS12636 | MetaboLights
ProteomicsProteome characterization of HCMV virus microenvironment
The control of host processes which influence cell-cell communication is central to determining the outcome of a virus infection in tissue. Despite this, it remains unclear how cells either in close or distant proximity to an infected cell differentially respond to the primary infection. Here, we es...
ORGANISM(S): Homo sapiens (Human) Human betaherpesvirus 5 
2023-05-11 | PXD038547 | Pride
Hcmv Innate immunity Membrane contact sites Mass spectrometry Virus microenvironment Cell cycle Susceptibility 
ProteomicsProteome characterization of HCMV virus microenvironment with addition of cidofovir
The control of host processes which influence cell-cell communication is central to determining the outcome of a virus infection in tissue. Despite this, it remains unclear how cells either in close or distant proximity to an infected cell differentially respond to the primary infection. Here, we es...
ORGANISM(S): Homo sapiens (Human) 
2023-05-11 | PXD040582 | Pride
Hcmv Innate immunity Membrane contact sites Mass spectrometry Virus microenvironment Cell cycle Cidofovir 
TranscriptomicsRegulation of GLI underlies a role for BET bromodomains in pancreatic cancer growth and the tumor microenvironment
Pancreatic ductal adenocarcinoma (PDAC) is extraordinarily chemoresistant and the abundant stromal content of these tumors contributes to the ineffective treatment of this disease. While the genetic alterations of PDAC have been well characterized, the epigenetic pathways regulating PDAC remain, fo...
ORGANISM(S): Homo sapiens 
2016-09-08 | E-GEOD-55209 | biostudies-arrayexpress
ModelsAlmuallem2020 - Virus-macrophage-tumour interactions in oncolytic viral therapies
This mathematical model of the role of the innate immune responses generated by macrophages in the context of anti-tumour oncolytic viral therapies is described in the publication: Nada Almuallem, Dumitru Trucu, Raluca Eftimie. "Oncolytic viral therapies and the delicate balance between virus-macrop...
2024-09-02 | BIOMD0000001033 | BioModels
Immuno-oncology 
GenomicsAn oncolytic virus–delivered TGFβ inhibitor overcomes the immunosuppressive tumor microenvironment
An oncolytic virus–delivered TGFβ inhibitor overcomes the immunosuppressive tumor microenvironment
PRJNA779090 | ENA
ProteomicsProximity biotinylation and LC-MSMS identification of the molecular microenvironment of coronavirus replication complexes
To investigate virus-host interactions at the site of coronavirus replication, we developed a biotin-based proximity labelling approach by engineering a promiscuous biotin ligase, BirA-R118G, within the coronavirus replication and transcription complex (RTC). BirA-R118G was fused to non-structural p...
ORGANISM(S): Murine hepatitis virus strain A59 Mus musculus (Mouse) 
2019-01-16 | PXD009975 | Pride
L929 mouse fibroblast Lc-msms Viral replication complex Bira-r118g Mouse hepatitis virus Bioid 
ProteomicsOLFM4 is a direct target of the cGAS-STING pathway and acts as an extracellular inhibitor for the Hippo signaling in EBV-associated cancer
To investigate protein components of MVs in EBVaGC, we collected clinical tissue samples of 3 EBV+ and 3 EBV- gastric cancer patients, and isolated MVs from these samples. Then performed 4D-label free quantitative proteomics analysis for each isolated MVs. Raw files of 6 samples are included in subp...
ORGANISM(S): Homo Sapiens 
2024-11-18 | PXD057977 |
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