Long Oligonucleotide Microarrays for African Green Monkey Gene Expression Profile Analysis
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE6982
PROVIDER: PRJNA99293 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Nonhuman primates including African Green Monkey (AGM) are important models for biomedical research. The information on monkey genomes is still limited and no versatile gene expression screening tool is available. We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes, Applied Biosystems-ABI) and short oligonucleotide arrays (25-mer, Affymetrix). Using the long oligonucleotide arrays we detected four times more AGM transcripts than with the short oligonucleotide technology. The number of detected transcripts was comparable to that detected using human RNA, with 87% of the detected genes being shared between both species. The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A activated CD4+ T cells versus non-activated T cells of two monkey species AGM and macaque. For both species, the genes showing the most significant changes in expression, such as IL-2R, were those known to be also regulated in human CD4+ T cell activation. Finally, tissue-specificity of the signals was established by comparing the transcription profiles of AGM brain and tonsil cells. In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles. Keywords: Defining a microarray platform to study the AGM transcriptome by cross-species and cross-platform comparison
2007-10-01 | GSE6982 | GEO
Project description:We will use the EMC/2012 strain of the novel beta Coronavirus called Middle East Respiratory Syndrome Coronavirus (MERS-CoV). It was initially passaged on Vero E6 cells in Saudi Arabia before being sequenced at the Erasmus Medical College in Rotterdam, Netherlands by Dr Ron Fouchier. We propose to perform a time course of infection of hCoV-EMC on MRC5 cells (Human Lung origin) and Vero cells (African Green Monkey Kidney cells). Both cell lines readily grow and replicate the virus. Importantly these cell lines show signs of Cytopathic effect (CPE), such as cell rounding and release from the petri dish that coincide with time points high virus replication demonstrating the effects of virus replication on the cells. Transcriptomic analysis will be performed after infection with MERS-CoV and SARS-CoV (Urbani strain) to compare the host gene induction that occurs during infection.
2015-11-19 | GSE56193 | GEO
Project description:In contrast to SIVagm, which does not cause disease in its natural simian host, HIV-1 expresses the accessory protein Vpu and encodes a Nef protein that fails to suppress T cell activation via down-modulation of CD3. Although both, Vpu and Nef have been implicated as pathogenicity determinants, their relevance for viral replication and disease progression in vivo has remained unclear. Here, we analyzed gene expression in African green monkeys infected with SIVagm chimeras differing in their expression of nef and/or vpu. We used microarrays to analyze global gene expression of African green monkeys in response to infection with SIVagm and found that the viral accessory nef and vpu genes co-determine the induction of distinct gene sets.
2018-03-02 | GSE103072 | GEO
Project description:We will use the EMC/2012 strain of the novel beta Coronavirus called Middle East Respiratory Syndrome Coronavirus (MERS-CoV). It was initially passaged on Vero E6 cells in Saudi Arabia before being sequenced at the Erasmus Medical College in Rotterdam, Netherlands by Dr Ron Fouchier. We propose to perform a time course of infection of hCoV-EMC on MRC5 cells (Human Lung origin) and Vero cells (African Green Monkey Kidney cells). Both cell lines readily grow and replicate the virus. Importantly these cell lines show signs of Cytopathic effect (CPE), such as cell rounding and release from the petri dish that coincide with time points high virus replication demonstrating the effects of virus replication on the cells. Transcriptomic analysis will be performed after infection with MERS-CoV and SARS-CoV (Urbani strain) to compare the host gene induction that occurs during infection. MRC5 and Vero E6 cells will be infected at an MOI of 0.1 and 3 and RNA harvested from cells at 24 and 48 post infection. RNA will be processed for library creation and sequenced on an Illumina Hiseq. Sequencing reads will be analyzed and compared across the time course and between each virus to identify common response pathways induced during infection as well as unique pathways specific to each virus.
2015-11-19 | E-GEOD-56193 | biostudies-arrayexpress
Project description:While many preclinical models of Alzheimer’s disease (AD) have been reported, none fully recapitulate the disease. In an effort to identify an appropriate preclinical disease model, we characterized age-related changes in two higher order species, the African Green Monkey (AGM) and the rhesus macaque. Gene expression profiles in the dorsolateral prefrontal cortex and the visual cortex showed age-related changes in AGMs that are strikingly reminiscent of AD, whereas aged rhesus were most similar to healthy elderly humans. Biochemically, age-related changes in AGM cerebrospinal fluid levels of tau, phospho-tau and amyloid beta were consistent with AD. Histologically, aged AGMs displayed pathological hallmarks of the disease, plaques, and two AGMs showed evidence of neurofibrillary tangle-like structures. We hypothesized and confirmed that AGMs have age-related cognitive deficits via a prefrontal cortex-dependent cognition test, and that symptomatic treatments which improve cognition in AD patients show efficacy in AGMs. These data suggest that the AGM could represent a novel and improved translational model to assist in the development of therapeutics for AD.
2018-02-01 | GSE108282 | GEO
Project description:Recently, long oligonucleotide (60-70mer) microarrays for two-color experiments have been developed and are gaining widespread use. In addition, when there is limited availability of mRNA from tissue sources, RNA amplification can and is being used to produce sufficient quantities of cRNA for microarray hybridization. Taking advantage of the selective degradation of RNA under alkaline conditions, we have developed a method to “strip” glass-based oligonucleotide microarrays that use fluorescent RNA in the hybridization, while leaving the DNA oligonucleotide probes intact and usable for a second experiment. Replicate microarray experiments conducted using stripped arrays showed high reproducibility, however, we found that arrays could only be stripped and reused once without compromising data quality. The intraclass correlation (ICC) between a virgin array and a stripped array hybridized with the same sample showed a range of 0.90-0.98, which is comparable to the ICC of two virgin arrays hybridized with the same sample. Using this method, once stripped oligonucleotide microarrays are usable, reliable, and should help to reduce costs. Keywords = Agilent microarray Keywords = Stripped arrays Keywords = Replicate reproducibility Keywords: other
2005-02-23 | GSE1706 | GEO
Project description:Epigenetic reprogramming leads to down regulation of CD4 and functional changes in African green monkey memory CD4+ T cells
| PRJNA801048 | ENA
Project description:Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria
| PRJNA99965 | ENA
Project description:A prototype oligonucleotide microarray was designed to detect and identify viable bacterial species with the potential to grow of common beer spoilage microorganisms from the genera Lactobacillus, Megasphaera, Pediococcus and Pectinatus. Probes targeted the intergenic spacer regions (ISR) between 16S and 23S rRNA, which were amplified in a combination of reverse transcriptase (RT) and polymerase chain reaction (PCR) prior to hybridization. This method allows the detection and discrimination of single bacterial species in a complex sample. Furthermore, microarrays using oligonucleotide probes targeting the ISR allow the distinction between viable bacteria with the potential to grow and non-growing bacteria. The results demonstrate the feasibility of oligonucleotide microarrays as a contamination control in food industry for the detection and identification of spoilage microorganisms within mixed population. Keywords: microarray, oligonucleotide, species-specific, detection, beer spoilage bacteria
2007-05-23 | GSE7840 | GEO
Project description:African green monkeys (AGMs) are a natural host for a lentivirus related to human immunodeficiency virus, simian immunodeficiency virus. SIV-infected AGM rarely progress to AIDS despite robust viral replication. Though multiple mechanisms are involved, a primary component is their ability to downregulate CD4 expression on mature helper CD4+ T cells, rendering these cells resistant to infection by SIV. These CD8aa+ T cells retain functional characteristics of helper CD4+ T cells while simultaneously aquiring abilities of cytoxic CD8ab+ T cells. To determine mechanisms underlying functional differences between T cell subsets in AGMs, chromatin accessibility in purified populations was determined by ATACseq. Differences in chromatin accessibility alone were sufficient to cluster cells by subtype, and acceesibility at the CD4 locus reflected changes in CD4 expression. DNA methylation at the CD4 locus also correlated with inaccessible chromatin. By associating accessible regions with nearby genes, gene expression was found to correlate with accessibility changes. T cell and immune system activation pathways were identified when comparing regions that changed accessibility from CD4+ T cells to CD8aa+ T cells. Different transcription factor binding sites are revealed as chromatin accessibility changes, and these differences may elicit downstream changes in differentiation. This comprehensive description of the epigenetic landscape of AGM T cells identified genes and pathways that could have translational value in therapeutic approaches recapitulating the protective effects CD4 downregulation.
2022-05-05 | GSE195520 | GEO