E-GEOD-7819
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA100049
PROVIDER: E-GEOD-7819 | ExpressionAtlas | 2015-10-22
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:JC virus (JCV) is a ubiquitous human polyomavirus that causes the demyelinating disease Progressive Multifocal Leukoencephalopathy (PML). JCV replicates in limited cell types in culture, predominantly in human glial cells. Thus, productive JCV infection is an indicator of the host cell transcription environment. Following introduction of a replication defective SV40 mutant that expressed large T protein into a heterogeneous culture of human fetal brain cells, multiple phenotypes became immortalized (SVG cells). A subset of SVG cells could support JCV replication. This mixed culture was called SVG cells. In the current study, clonal cell lines were selected from the original SVG cell culture. The SVG-5F4 clone showed low levels of viral growth. The SVG-10B1 clone was highly permissive for JCV DNA replication and gene expression. Microarray analysis revealed that viral infection did not significantly change gene expression in these cells. More resistant 5F4 cells expressed high levels of transcription factors known to inhibit JCV transcription. Interestingly, 5F4 cells highly expressed RNA of markers of Bergman or radial glia and 10B1 cells had high expression of markers of immature glial cells and activation of transcription regulators important for stem/progenitor cell self-renewal. These SVG-derived clonal cell lines provide a biologically relevant model to investigate cell type differences in JCV host range and pathogenesis, as well as neural development. 13 Human samples: 3 SVG 10B1 clones 14 days post mock-infection, 3 SVG 10B1 clones 14 days post JCV Mad-4 strain infection, 3 SVG 5F4 clones 14 days post mock-infection, 4 SVG 5F4 clones 14 days post JCV Mad-4 strain infection.
2013-10-17 | E-GEOD-45639 | biostudies-arrayexpress
Project description:We performed gene expression profiling by Affymetrix primeview array in both TAE sensitive, resistant and JQ1-treated resistant Kelly cells.
2019-08-07 | GSE103083 | GEO
Project description:JC virus (JCV) is a ubiquitous human polyomavirus that causes the demyelinating disease Progressive Multifocal Leukoencephalopathy (PML). JCV replicates in limited cell types in culture, predominantly in human glial cells. Thus, productive JCV infection is an indicator of the host cell transcription environment. Following introduction of a replication defective SV40 mutant that expressed large T protein into a heterogeneous culture of human fetal brain cells, multiple phenotypes became immortalized (SVG cells). A subset of SVG cells could support JCV replication. This mixed culture was called SVG cells. In the current study, clonal cell lines were selected from the original SVG cell culture. The SVG-5F4 clone showed low levels of viral growth. The SVG-10B1 clone was highly permissive for JCV DNA replication and gene expression. Microarray analysis revealed that viral infection did not significantly change gene expression in these cells. More resistant 5F4 cells expressed high levels of transcription factors known to inhibit JCV transcription. Interestingly, 5F4 cells highly expressed RNA of markers of Bergman or radial glia and 10B1 cells had high expression of markers of immature glial cells and activation of transcription regulators important for stem/progenitor cell self-renewal. These SVG-derived clonal cell lines provide a biologically relevant model to investigate cell type differences in JCV host range and pathogenesis, as well as neural development.
2013-10-17 | GSE45639 | GEO
Project description:The goal of this study was to determine how an HIV quasispecies is maintained in the face of selection. We deep sequenced the HIV provirus from cell populations as well as single cells at different time points from in vitro evolution experiments and found that when a less fit and more fit infect the same cell, they share components (complmentation) and therefore allow the less fit to perpetuate. We reproduced a quasispecies to an HIV reverse transcriptase inhibitor. The drug resistant genotype never completely supplanted the drug sensitive genotype, which stabilized at about 20% of viral sequences. Single-cell sequencing showed that resistant genotype frequency plateaued when cells were co-infected with sensitive and resistant genotypes, suggesting a sharing of viral proteins in co-infected cells (complementation), masking genotypic differences. To test if complementation can confer phenotypic drug resistance, we co-transfected fluorescently labelled molecular clones of sensitive and resistant HIV and observed drug resistance in genotypically sensitive virus from co-transfected cells. Resistant virus preferentially co-infected cells with drug sensitive HIV, explaining initiation of co-infections. Modelling showed that a stable quasispecies could form at the experimental multiplicities of infection. Conclusions: Complementation can lead to a quasispecies in infection environments where multiple infections per cell are common
2020-05-13 | GSE150390 | GEO
Project description:Human EMT PCR array PCR array data for expression of EMT genes in MCF-7 cells after co-culture with insulin sensitive (IS) and insulin resistant (IR) adipocytes
2021-10-22 | GSE186364 | GEO
Project description:To systematically examine host-virus interaction in HIV infection, we used isobaric tag-based quantitative mass spectrometry to perform a proteomic profiling of HIV infection of human primary CD4 T cells.
| MSV000082987 | MassIVE
Project description:Analysis of death triggering pathways activated by experimental Zika virus infection in SH-SY5Y cells by expression profiling of 42 genes related to survival, anti-apoptotic and proapoptotic responses, and death receptors pathway, and 06 endogenous control genes. Commercially available neuroblastoma SH-SY5Y cells were grown in vitro, experimentally infected with Zika virus (MOI 0.5), and MOCK- and ZIKV-infected cells were harvested at 1 and 2 days post-infection. We used TaqMan ™ Array Human Apoptosis via Death Receptors (Thermo Fisher Scientific, MA, USA) to quantitate gene expression during ZIKV infection in SH-SY5Y cells.
2021-12-01 | GSE162096 | GEO
Project description:<p>Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to identify lipid biomarkers for the resistance of the bloom-forming alga <em>Emiliania huxleyi</em> to its specific virus, <em>E. huxleyi</em> virus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistant <em>E. huxleyi</em> strains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers in <em>E. huxleyi</em> isolates collected from induced <em>E. huxleyi</em> blooms and in samples collected during an open-ocean <em>E. huxleyi</em> bloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition of <em>E. huxleyi</em> cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and coevolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.</p>
2023-06-12 | MTBLS3323 | MetaboLights
Project description:SVGR2 cells are glial cells which are derived from SVG-A cells. They were created by subjecting SVG-A cells to multiple rounds of lytic infection by the human polyomavirus JCV. SVGR2 cells are the cells that survived this process and are resistant to JCV infection. This experiment was designed to identify gene expression differences that may be responsible for SVGR2 resistance to JCV. Keywords: Cell type
2007-05-25 | GSE7819 | GEO
Project description:Expression profiling of nasopharyngeal carcinoma patients comparing radio-sensitive samples with radio-resistant samples. Two condition-experiments, radio-sensitive and radio-resistant nasopharyngeal carcinoma patients. Biological replicates: 8 radio-sensitive, 12 radio-resistant, different donors in the same hospital. One patient per array.
2013-09-21 | E-GEOD-32389 | biostudies-arrayexpress