Viruses
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA106189 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Cardioviruses are a genus of picornaviruses that cause severe illnesses in rodents, but little is known about the prevalence, diversity, or spectrum of disease of such agents among humans. We report the identification of a group of human cardioviruses that have been detected and cloned directly from patient specimens (Chiu and DeRisi, et al, PNAS, 2008). This series includes 9 arrays (both raw and normalized data) used to detect cardioviruses in human respiratory and stool specimens. The arrays employed here are capable of pan-viral detection (Wang and DeRisi, et al., PNAS, 2002). Keywords: viral detection, cardiovirus, TMEV, gastroenteritis The series includes 3 arrays from respiratory samples and 6 arrays from stool samples. Among the 3 arrays from respiratory sample, 1 array has a signature for an adenovirus, 1 array has a signature for human metapneumovirus, and 1 array has a signature for cardiovirus UC1 (see Chiu and DeRisi, et al., PNAS, in 2008). All 6 arrays from stool samples are cardiovirus-positive; some show evidence of dual infection with other gastroenteritis viruses (i.e. norovirus, rotavirus, etc.). Data in Sample records fed to E-Predict (Urisman, et al, Genome Biology, 2005) E-Predict normalization metrics Array Normalization: Sum E-Matrix Normalization: Quadratic Distance Metric: Pearson Uncentered
2008-09-17 | E-GEOD-11569 | biostudies-arrayexpress
Project description:Cardioviruses are a genus of picornaviruses that cause severe illnesses in rodents, but little is known about the prevalence, diversity, or spectrum of disease of such agents among humans. We report the identification of a group of human cardioviruses that have been detected and cloned directly from patient specimens (Chiu and DeRisi, et al, PNAS, 2008). This series includes 9 arrays (both raw and normalized data) used to detect cardioviruses in human respiratory and stool specimens. The arrays employed here are capable of pan-viral detection (Wang and DeRisi, et al., PNAS, 2002). Keywords: viral detection, cardiovirus, TMEV, gastroenteritis
2008-09-17 | GSE11569 | GEO
Project description:Human Norwalk virus (HuNoVs), the most common etiological agents of acute gastroenteritis, are genetically diverse RNA viruses that frequently cause mass food poisoning internationally. In this study, we developed a parallel reaction monitoring (PRM) assay to simultaneously detect and identify representative peptides derived from VP1 in six different HuNoV genotypes using a high-resolution mass spectrometer. An optimized protocol was also used to detect and quantify VP1 protein in human stool specimens. This method is expected to become a new tool for studying the molecular epidemiology of HuNoV and to shed new light on targeted proteomics in clinical practice.
2023-02-21 | PXD033981 | JPOST Repository
Project description:This series includes 278 microarrays used to detect respiratory viruses in a set of nasopharyngeal lavage specimens from children with respiratory tract infections Objective: To assess the utility of a pan-viral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections. Study Design: The Virochip was compared to conventional clinical direct fluorescent antibody (DFA) and PCR-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. Results: The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity 85-90%, specificity 99%, PPV 94-96%, NPV 97-98%) in the detection of respiratory syncytial virus, influenza A, and rhino-/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. Conclusions: Given its favorable sensitivity and specificity profile and greatly expanded spectrum of detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric respiratory tract infections. Keywords: viral detection The series includes 278 clinical specimens
2010-05-26 | E-GEOD-10294 | biostudies-arrayexpress
Project description:Understanding gene expression by bacteria during the actual course of human infection may provide important insights into microbial pathogenesis. In this study, we evaluated the transcriptional profile of Vibrio cholerae, the causative agent of cholera, in clinical specimens from cholera patients. We collected samples of human stool and vomitus that were positive by dark-field microscopy for abundant vibrios and used a microarray to compare gene expression in organisms recovered directly from the early and late stages of human infection. Our results reveal that V. cholerae gene expression within the human host environment differs from patterns defined in in vitro models of pathogenesis. tcpA, the major subunit of the essential V. cholerae colonization factor, was significantly more highly expressed in early compared with late infection; however, the genes encoding cholera toxin were not highly expressed in either phase of human infection. Furthermore, expression of the virulence regulators, toxRS and tcpPH, was uncoupled. Interestingly, the pattern of gene expression indicates that the human upper intestine may be a uniquely suitable environment for the transfer of genetic elements that are important in the evolution of pathogenic strains of V. cholerae. These findings provide a more detailed assessment of the transcriptome of V. cholerae in the human host than previous studies of organisms in stool alone and have implications for cholera control and the design of improved vaccines. The V. cholerae microarray consists of 3,890 full-length PCR products representing the annotated open reading frames from the initial release of the V. cholerae N16961 genome. Each labeling and hybridization was performed in duplicate. Genomic DNA was used as a universal internal control for the quality of the microarray and to allow for the comparison of results across multiple experiments. Data were normalized using locally-weighted regression (Lowess) to obtain the relative abundance of each transcript as an intensity ratio with respect to that of genomic DNA. High correlation coefficients were observed between technical replicates (Pearsonâs correlation coefficient (r) > 0.80) and between results of separate clinical specimens of vomitus (r > 0.77) and of stool (r > 0.80). Hence, the results from the two clinical vomitus specimens and the five clinical stool specimens were pooled. Fold changes for the relative expression of a given gene between the two clinical specimens were calculated by dividing the normalized median intensity ratios with respect to genomic DNA.
2010-06-09 | E-GEOD-2775 | biostudies-arrayexpress
Project description:respiratory viruses in human nasal-throat swabs Raw sequence reads
| PRJNA639353 | ENA
Project description:Human metapneumovirus strain associated with critical respiratory illness in an elderly male with leukemia Stanford HMPV
| PRJNA97529 | ENA
Project description:This series includes 278 microarrays used to detect respiratory viruses in a set of nasopharyngeal lavage specimens from children with respiratory tract infections Objective: To assess the utility of a pan-viral DNA microarray platform (Virochip) in the detection of viruses associated with pediatric respiratory tract infections. Study Design: The Virochip was compared to conventional clinical direct fluorescent antibody (DFA) and PCR-based testing for the detection of respiratory viruses in 278 consecutive nasopharyngeal aspirate samples from 222 children. Results: The Virochip was superior in performance to DFA, showing a 19% increase in the detection of 7 respiratory viruses included in standard DFA panels, and was similar to virus-specific PCR (sensitivity 85-90%, specificity 99%, PPV 94-96%, NPV 97-98%) in the detection of respiratory syncytial virus, influenza A, and rhino-/enteroviruses. The Virochip also detected viruses not routinely tested for or missed by DFA and PCR, as well as double infections and infections in critically ill patients that DFA failed to detect. Conclusions: Given its favorable sensitivity and specificity profile and greatly expanded spectrum of detection, microarray-based viral testing holds promise for clinical diagnosis of pediatric respiratory tract infections. Keywords: viral detection
2008-07-09 | GSE10294 | GEO
Project description:Distal gut bacteria play a pivotal role in the digestion of dietary polysaccharides by producing a large number of carbohydrate-active enzymes (CAZymes) that the host otherwise does not produce. We report here the design of a high density custom microarray that we used to spot non-redundant DNA probes for more than 6,500 genes encoding glycoside hydrolases and lyases selected from 174 reference genomes from distal gut bacteria. The custom microarray was tested and validated by the hybridization of bacterial DNA extracted from the stool samples of lean, obese and anorexic individuals. Our results suggest that a microarray-based study can detect genes from low-abundance bacteria better than metagenomic-based studies. A striking example was the finding that a gene encoding a GH6-family cellulase was present in all subjects examined, whereas metagenomic studies have consistently failed to detect this gene in both human and animal gut microbiomes. In addition, an examination of eight stool samples allowed the identification of a corresponding CAZome core containing 46 families of glycoside hydrolases and polysaccharide lyases, which suggests the functional stability of the gut microbiota despite large taxonomical variations between individuals.
2013-10-28 | GSE51760 | GEO
Project description:Total DNA was extracted from stool specimens, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.
2022-08-24 | GSE206807 | GEO