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PROVIDER: PRJNA645177 | 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
2008-09-17 | GSE11569 | GEO
Project description:In animals, microRNA (miRNA) biogenesis begins with cotranscriptional cleavage of the primary (pri-)miRNA by Microprocessor. Cotranscriptional splicing has been shown to influence Microprocessor cleavage for miRNAs hosted in introns of protein coding pri-miRNAs, but the impact of splicing on production of miRNAs hosted in long noncoding (lnc)RNAs is largely unknown. Here, we investigated the role of splicing in the biogenesis of miR-122, a lncRNA-hosted, highly expressed, medically important, liver-specific miRNA. We found that splicing inhibition by the SF3B1 inhibitor Pladienolide B (PlaB) led to strong and rapid reduction in transcription of endogenous, but not plasmid-encoded, pri-miR-122, resulting in reduced production of mature miR-122. To allow detection of rapid changes in miRNA biogenesis despite the high stability of mature miRNAs, we used SLAMseq to globally quantify the effects of short-term splicing inhibition on miRNA synthesis. We observed an overall decrease in biogenesis of mature miRNAs following PlaB treatment. Surprisingly, miRNAs derived from different genomic locations were similarly affected. Together, this study provides new insight into the emerging role for splicing in transcription, demonstrating novel biological importance in promotion of miR-122 biogenesis from a lncRNA, and shows that splicing is important for global miRNA biogenesis.
2024-06-05 | GSE240904 | GEO
Project description:BACKGROUND: 50% to 80% of asthma exacerbations are precipitated by viral upper respiratory tract infections (RTI), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood due to the limited scope and throughput of conventional viral detection methods. METHODS: We investigated the capability of the Virochip, a DNA microarray-based viral detection platform, to characterize the viral diversity in RTIs in asthmatic and non-asthmatic adults. RESULTS: The Virochip detected viruses in a higher proportion of samples (65%) than culture isolation (17%), while exhibiting high concordance (98%), sensitivity (97%) and specificity (98%) with pathogen-specific PCR. A similar spectrum of viruses was identified in the RTIs from each patient subgroup; however, unexpected diversity among the coronaviruses (HCoVs) and HRVs was revealed. All but one of the HCoVs corresponded to the newly-recognized HCoV-NL63 and HCoV-HKU1 viruses, and over 20 different serotypes of HRVs were detected, including a set of 5 divergent isolates that form a distinct genetic subgroup. CONCLUSIONS: The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger scale studies will be necessary to determine if particular substrains of viruses confer an elevated risk of asthma exacerbation Keywords: Virus detection
2007-11-07 | GSE7301 | GEO
Project description:BACKGROUND: 50% to 80% of asthma exacerbations are precipitated by viral upper respiratory tract infections (RTI), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood due to the limited scope and throughput of conventional viral detection methods. METHODS: We investigated the capability of the Virochip, a DNA microarray-based viral detection platform, to characterize the viral diversity in RTIs in asthmatic and non-asthmatic adults. RESULTS: The Virochip detected viruses in a higher proportion of samples (65%) than culture isolation (17%), while exhibiting high concordance (98%), sensitivity (97%) and specificity (98%) with pathogen-specific PCR. A similar spectrum of viruses was identified in the RTIs from each patient subgroup; however, unexpected diversity among the coronaviruses (HCoVs) and HRVs was revealed. All but one of the HCoVs corresponded to the newly-recognized HCoV-NL63 and HCoV-HKU1 viruses, and over 20 different serotypes of HRVs were detected, including a set of 5 divergent isolates that form a distinct genetic subgroup. CONCLUSIONS: The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger scale studies will be necessary to determine if particular substrains of viruses confer an elevated risk of asthma exacerbation This SuperSeries is composed of the SubSeries listed below.
2007-11-07 | GSE8053 | GEO
Project description:BACKGROUND: 50% to 80% of asthma exacerbations are precipitated by viral upper respiratory tract infections (RTI), yet the influence of viral pathogen diversity on asthma outcomes is poorly understood due to the limited scope and throughput of conventional viral detection methods. METHODS: We investigated the capability of the Virochip, a DNA microarray-based viral detection platform, to characterize the viral diversity in RTIs in asthmatic and non-asthmatic adults. RESULTS: The Virochip detected viruses in a higher proportion of samples (65%) than culture isolation (17%), while exhibiting high concordance (98%), sensitivity (97%) and specificity (98%) with pathogen-specific PCR. A similar spectrum of viruses was identified in the RTIs from each patient subgroup; however, unexpected diversity among the coronaviruses (HCoVs) and HRVs was revealed. All but one of the HCoVs corresponded to the newly-recognized HCoV-NL63 and HCoV-HKU1 viruses, and over 20 different serotypes of HRVs were detected, including a set of 5 divergent isolates that form a distinct genetic subgroup. CONCLUSIONS: The Virochip can detect both known and novel variants of viral pathogens present in RTIs. Given the diversity detected here, larger scale studies will be necessary to determine if particular substrains of viruses confer an elevated risk of asthma exacerbation Keywords: Virus detection
2007-11-07 | GSE8029 | GEO
Project description:Gastrodia confusoides habitat fungal diversity
| PRJNA778455 | ENA
Project description:Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods
| PRJNA552605 | ENA
Project description:The goal of this study was to identify the key functions of the six main symbionts that are hosted in gills of the marine bivalve, Idas modiolaeformis, which lives at deep-sea hydrocarbon seeps and wood falls in the Eastern Atlantic Ocean and the Mediterranean Sea. These symbionts include the main autotrophic methane- and sulfur-oxidizing lineages (Methyloprofundus, Thioglobus, Thiodubillierella), as well as a Methylophagaceae methylotrophic autotroph, a flavobacterial degrader of complex polysaccharides Urechidicola and a Nitrincolaceae heterotroph that specializes in degradation of nitrogen-rich compounds such as peptides and nucleosides. Four I. modiolaeformis individuals were preserved in RNAlater following retrieval from a brine pool habitat in the Eastern Mediterranean at 1,150 m water depth (32° 13.4' N 34° 10.7' E), using a remotely-operated vehicle. RNAlater was discarded after 24 hours, and the specimens were kept at -80°C until DNA/RNA/protein co-extraction using the AllPrep DNA/RNA/Protein Mini Kit (Cat. No. 80004, Qiagen).
2023-07-20 | PXD040273 | Pride
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