Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33276 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ribeiro2019.vcf.gz | Vcf | |||
| ribeiro2019.vcf.gz.tbi | Vcf |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Host anti-viral factors are essential for controlling SARS-CoV-2 infection but remain largely unknown due to the biases of previous large-scale studies toward pro-viral host factors. To fill in this knowledge gap, we perform a genome-wide CRISPR dropout screen and integrate analyses of the multi-omics data of the CRISPR screen, genome-wide association studies, single-cell RNA-Seq, and host-virus proteins or protein/RNA interactome. This study uncovers many host factors that are missed by previous studies, including the components of V-ATPases, ESCRT, and N-glycosylation pathways that modulate viral entry and/or replication. The cohesin complex is also identified as an anti-viral pathway, suggesting an important role of three-dimensional chromatin organization in mediating host-viral interaction. Furthermore, we discover another anti-viral regulator KLF5, a transcriptional factor involved in sphingolipid metabolism, which is up-regulated and harbored genetic variations linked to COVID-19 patients with severe symptoms. Anti-viral effects of three identified candidates (DAZAP2/VTA1/KLF5) are confirmed individually. Molecular characterization of DAZAP2/VTA1/KLF5-knockout cells highlights the involvement of genes related to the coagulation system in determining the severity of COVID-19. Together, our results provide wealthy resources for understanding the host anti-viral network during SARS-CoV-2 infection and may help develop new countermeasure strategies.
2023-10-30 | GSE246452 | GEO
Project description:Host immunogenetics and association with severity of Blastomyces infection
| PRJNA1020973 | ENA
Project description:Host immunogenetics and association with severity of Blastomyces infection
| PRJNA1020975 | ENA
Project description:To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. To further exploring the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases.
2023-01-17 | GSE211972 | GEO
Project description:Dengue virus (DENV) infection is a major emerging disease in tropical and subtropical countries and the influence of host genetics during early phases of infection remains to be fully elucidated. Here we use dendritic cells (DCs) and macrophages from healthy individuals to establish inter-individual variability in DENV infection and antibody-mediated enhancement (ADE). We show that host-related factors determine the severity of the infection rate both in DENV-infected DCs and macrophages following ADE. We then correlate the inter-individual variability in infection rates with genome-wide transcript abundance measured by RNA sequencing in DCs following DENV infection. We report 190 host-related transcripts in DCs that correlate markedly with infection rates that form an ubiquitin-mediated antiviral network. Furthermore, these transcripts are enriched for glycolysis, which we show is critical for the early phases of infection. Among virus induced transcripts (i.e. significant correlation only after DENV), we identify DUSP10 as the best indicator of the severity of infection. These results indicate the importance of host genetics in shaping the severity of DENV infection rates in DCs and identify novel potential DENV-susceptibility targets.
2021-02-26 | GSE111330 | GEO
Project description:The development of cervical cancer is initiated by human papillomavirus (HPV) infection, and involves both viral and host genetic factors. Genome-wide association studies (GWAS) of cervical cancer have identified associations in the HLA locus and two loci outside HLA, but the principal genes that control infection and pathogenesis have not been identified. In the present study, we performed GWAS of cervical cancer in East Asian populations, involving 2609 cases and 4712 controls in the discovery stage, 1461 cases and 3295 controls in the follow-up stage.
| EGAS00001003199 | EGA
Project description:Phenome-wide association study maps genetic variation in epigenetic factors with human complex diseases
| PRJNA564405 | ENA
Project description:The biotrophic fungal pathogen Ustilago maydis cause common smut in maize, and lead to gall formation on all aerial organs, especially on maize kernel thus reduce yield. The interaction of U. maydis with maize is a well-established model to study the interaction between maize and biotrophic pathogen. U. maydis infection could activate host immune responses including: ROS accumulation, protease activation, salicylic acid signaling. U. maydis employ several strategies to overcome maize immune response, thus initial the biotrophic interaction with host. It has been suggested that genetic factors of maize host affected the disease severity of U. maydis infection, here we investigated the transcriptome profile of resistance and susceptible maize lines upon U. maydis infection, thus propose candidate maize genes involved in the defense response in maize to corn smut cause by U. maydis.
2021-04-15 | GSE172071 | GEO
Project description:Epigenome-Wide Association Study of COVID-19 Severity with Respiratory Failure
| PRJNA713800 | ENA
Project description:<p>A prospective multi-year clinical translational study including three cohorts of term infants experiencing their first Respiratory Syncytial Virus (RSV) season. All infants are less than or equal to nine months of age at study entry. The three subject cohorts represent the full spectrum of RSV disease severity and include a birth cohort, a cohort of infants hospitalized for RSV disease and infants evaluated at ambulatory settings for RSV infection. All infants are followed longitudinally and evaluated at recognition of acute RSV infection and twice during convalescence. Innate and adaptive immune status are comprehensively measured in association with clinical, environmental, viral, and bacteriologic factors. Genome-wide expression is assessed in the nasal airways, and in sorted peripheral blood lymphocytes. The study goal is to Identify host responses to RSV infection and factors associated with severe disease. </p>
| phs001201 | dbGaP