Comparative genome sequencing of wild type rhesus cytomegalovirus (RhCMV) with a recombinant RhCMV lacking ORF 178
Ontology highlight
ABSTRACT:
ORGANISM(S): Macacine herpesvirus 3
SUBMITTER: Rebecca Richards
PROVIDER: E-GEOD-20308 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Recombinant RhCMV was created to study super-infection of Rhesus macaques. These viruses (RhCMV Δ178;RhCMV Δ182-189;RhCMV Δ178Δ182-189) were co-hybridized with a wild-type BAC-derived RhCMV to a RhCMV tiling array to ensure that there were no additional mutations beyond the intended deleted regions.
2010-02-19 | GSE20308 | GEO
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2021-04-22 | GSE152338 | GEO
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Project description:Melanomas are often infiltrated by activated inflammatory cells. Thus, melanoma cells are very likely stimulated by inflammatory cytokines. In order to assess the impact of common inflammatory cytokines, we investigated the gene expression profile of melanoma cell lines before and after cytokine treatment in vitro. Experiment Overall Design: 5 human melanoma cell lines were treated with either IFN-α 1,000 U/ml, IFN-γ 100 U/ml or TNF-α 10 ng/ml for 72 hours, or were left untreated. We analyzed their expression profile with Affymetrix expression arrays.
2009-12-19 | E-GEOD-19428 | biostudies-arrayexpress
Project description:In this study, we explored x-inactivation in monkey embryos (ICM and TE separately) and pluripotent stem cells (IVF derived ES, SCNT-derived ES and monkey iPS) To elucidate x-inactivation in experimentally reprogrammed pluripotent cells, we derived pluripotent stem cells by both SCNT and iPS approaches from same parental skin fibroblasts. We also compared gene patterns of those cells to IVF-derived counterpart. The transcriptomes of rhesus monkey embryonic stem cell lines derived by both SCNT (CRES) and iPS (RiPS) from same monkey skin fibroblasts were compared each other. Both experimentally reprogrammed cells were also compared with IVF-derived counterpart (ORMES23). Finally, the adult somatic skin fibroblasts were analyzed. Three biological replicates of each cell line (A, B, C) were analyzed.
2012-08-31 | E-GEOD-36252 | biostudies-arrayexpress
Project description:This is a clinical study with an orally administered drug, BDTX-189 in participants with advanced solid tumors that have select mutations or alterations in human epidermal growth factor receptor 2 (HER2/ErbB2) genes or epidermal growth factor receptor (EGFR/ErbB1). The main goals of this study are to:
* Find the recommended dose of BDTX-189 that can be given safely to participants
* Learn more about the side effects of BDTX-189
* Learn what the body does to BDTX-189 after it has been taken (pharmacokinetics or PK)
* Determine the antitumor activity of BDTX-189 in participants with select allosteric ErbB gene mutations
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Project description:The epidermal growth factor receptor (EGFR) is overexpressed in approximately 90% of head and neck squamous cell carcinomas (HNSCC), and molecularly targeted therapy against the EGFR with the monoclonal antibody cetuximab modestly increases overall survival in head and neck cancer patients. We hypothesize that co-signaling through additional pathways limits the efficacy of cetuximab and EGFR-specific tyrosine kinase inhibitors (TKIs) in the clinical treatment of HNSCC. Analysis of gene expression changes in HNSCC cell lines treated 4 days with TKIs targeting EGFR and/or fibroblast growth factor receptors (FGFRs) identified transforming growth factor beta 2 (TGF-β2) induction in the three cell lines tested. Measurement of TGF-β2 mRNA validated this observation and extended it to additional cell lines. Moreover, TGF-β2 mRNA was increased in primary patient HNSCC xenografts treated for 4 weeks with cetuximab, demonstrating in vivo relevance of these findings. Functional genomics analyses with shRNA libraries identified TGF-β2 and TGF-β receptors (TGFβRs) as synthetic lethal genes in the context of TKI treatment. Further, direct RNAi-mediated silencing of TGF-β2 inhibited cell growth, both alone and in combination with TKIs. Also, a pharmacological TGFβRI inhibitor similarly inhibited basal growth and enhanced TKI efficacy. In summary, the studies support a TGF-β2-TGFβR pathway as a TKI-inducible growth pathway in HNSCC that limits efficacy of EGFR-specific inhibitors. HNSCC cell lines treated 4 days with TKIs targeting EGFR and/or fibroblast growth factor receptors (FGFRs) identified transforming growth factor beta 2 (TGF-β2) induction in the three cell lines tested
2016-03-22 | E-GEOD-67500 | biostudies-arrayexpress
Project description:The purpose of this screen was to identify synthetic lethal targets in FANCA-deficient cells.
2021-05-24 | E-MTAB-9802 | biostudies-arrayexpress
Project description:Aging of population is a great challenge of healthcare. In china, the number of the elderly is rapidly growing, and it was estimated that there will be approximately 400 million citizens above 65 years old in 2050.Study on the changes of brain during aging may help elucidate the mechanism of the pathological process, and hence prevent or treat these neurological diseases.Rhesus macaque (Macaca mulatta) and human have a genetic homology of 95%, and their anatomy structures or physiological process are highly similar, which make rhesus macaque one of the most important nonhuman primate models.Thus, the comparison between the change of protein profile during aging in human and rhesus macaque is still necessary, and the characteristics of proteins that are conservative or divergent are of interest.The aim of the(our) study is to identify the conservative changes of pathways during aging, and to reveal the potential difference between human and rhesus macaque so that relevant studies based on primate models can be interpreted more accurately.
2020-06-25 | PXD013597 | Pride
Project description:Lassa fever virus is a zoonotic pathogen that plagues the endemic areas of West Africa. Rhesus macaques infected with a related arenavirus, LCMV-WE, serve as a model for Lassa-infection of human beings. Using a dose similar to that expected from a needle-stick, monkeys experience an early pre-viremic phase (day 1-3), a viremic phase with febrile onset (day 4-7), and, like human beings who succumb, they die within two weeks. Our goal was to monitor changes in gene expression that parallel disease progression in an effort to 1) identify genes with altered expression after infection, 2) identify genes that could discriminate between a virulent and non-virulent infection, and 3) identify genes encoding products that could serve as treatment targets for FDA-approved pharmaceuticals. Genes related to all three of these categories have been identified and some have been given preliminary validation by quantitative PCR and proteomic studies. These genes will be valuable candidates for future validation as prognostic biomarkers; We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process. Experiment Overall Design: Rhesus macaques inoculated with a lethal dose of LCMV-WE were used to model human infection with Lassa fever virus (Lukashevich et al 2002, 2003; Rodas et al 2004). To identify molecular events that occur during the first few days of virus exposure, we monitored gene expression in peripheral blood mononuclear cell (PBMC) samples by microarray analysis. Approximately 150 samples from 23 different rhesus macaques (Table 1) were hybridized to Affymetrix U133 chips. Experiment Overall Design: Affymetrix U133 arrays cover the entire human genome with approximately 54,000 gene fragments representing approximately 22,000 genes. The use of these human arrays for macaque transcriptome analysis has been validated by other laboratories (Ace et al, 2004 Wang et al, 2004), i.e. 99.8% of the array elements for which human DNA gave a signal >1.4-fold over background were also >1.4 over background for macaque DNA (Rubins et al, 2004). LCMV-infected blood samples were compared to uninfected controls and genes with over two-fold change in expression were designated âdifferentially expressedâ (Fig. 1). Thus, out of 54,000 elements, 8410 (16%) were differentially regulated with a >2-fold change in expression [supplementary Table 1 has these genes in order of the magnitude of their differential expression]. Experiment Overall Design: Virus was detectable in these monkeys at day 4 after infection by plaque assay and by RT-PCR of blood cDNA (Djavani et al 2005). Although virus is replicating in monocytes, endothelial cells, liver, spleen, and peripheral lymphoid organs soon after inoculation (Rai et al, 1997; Lukashevich et al, 2002), virus is not detectable in the circulation for the first three days. Thus we define the early, pre-viremic stage as days 1-3, and a later viremic stage as days 4-7. Although the LCMV-Armstrong strain replicated as well in cell culture as LCMV-WE, the LCMV-Arm-infected monkeys did not experience viremia, i.e. viral nucleic acid were detected in tissues but virus loads were not high enough to be detected in the circulation. The Arm-infected monkeys resisted a lethal challenge with LCMV-WE, further confirming that they had been productively infected (Rodas et al, 2004). An overview of gene expression in monkeys shows a trend to down-regulate genes at the onset of viremia followed by a sharp increase in up-regulated genes. Those monkeys that did not experience viremia (Armstrong-infected) showed no dramatic down-regulation trend (Fig. 1). Over the entire study period of 7 days, the number of down-regulated genes in the WE-infected macaques was significantly more than the number seen in the Arm-infected monkeys (p < 0.005).
2008-06-14 | E-GEOD-5790 | biostudies-arrayexpress