Ontology highlight
ABSTRACT:
PROVIDER: PRJNA508475 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8282460_1.fastq.gz | Fastqsanger.gz | |||
| SRR8282460_2.fastq.gz | Fastqsanger.gz | |||
| SRR8282461_1.fastq.gz | Fastqsanger.gz | |||
| SRR8282461_2.fastq.gz | Fastqsanger.gz | |||
| SRR8282462_1.fastq.gz | Fastqsanger.gz |
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Project description:One of the cornerstones of an effective biodefense strategy is the ability to detect infectious agents with a high degree of sensitivity and specificity in the context of a complex sample background. The nature of the B. anthracis genome, however, renders specific detection difficult, due to close homology with B. cereus and B. thuringiensis. We therefore elected to determine the efficacy of next-generation sequencing analysis and microarrays for detection of B. anthracis in an environmental background. We applied next-generation sequencing to titrated genome copy numbers of B. anthracis in the presence of background nucleic acid extracted from aerosol and soil samples. We found next-generation sequencing to be capable of detecting as few as 10 genomic equivalents of B. anthracis DNA per nanogram of background nucleic acid. Detection was accomplished by mapping reads to either a defined subset of reference genomes or to the full GenBank database. Moreover, sequence data obtained from B. anthracis could be reliably distinguished from sequence data mapping to either B. cereus or B. thuringiensis. We also demonstrated the efficacy of a microbial census microarray in detecting B. anthracis in the same samples, representing a cost-effective and high-throughput approach, complementary to next-generation sequencing. This Series contains the NimbleGen array data only (no next-generation sequencing data). B. anthracis DNA was spiked at 6 different concentrations (1, 10, 100, 1000, 10000 and 100000 genome copies) into 1 ng of background nucleic acids extracted either from a soil sample or from an aerosol (air filter) sample. Two replicates of each combination of B. anthracis copy number and background sample were analyzed.
2013-06-27 | E-GEOD-48316 | biostudies-arrayexpress
Project description:Airborne transmission of SARS-CoV-2 aerosol remains contentious. Importantly, whether cough or breath-generated bioaerosols can harbor viable and replicating virus remains largely unclarified. We perform size-fractionated aerosol sampling (Andersen cascade impactor) and evaluate viral culturability in human cell lines (infectiousness), viral genetics, and host immunity in ambulatory participants with COVID-19. Sixty-one percent (27/44) and 50% (22/44) of participants emitted variant-specific culture-positive aerosols <10μm and <5μm, respectively, for up to 9 days after symptom onset. Aerosol culturability is significantly associated with lower neutralizing antibody titers, and suppression of transcriptomic pathways related to innate immunity and the humoral response. A nasopharyngeal Ct <17 rules-in ~40% of aerosol culture-positives and identifies those who are probably highly infectious. A parsimonious three transcript blood-based biosignature is highly predictive of infectious aerosol generation (PPV> 95%). There is considerable heterogeneity in potential infectiousness i.e., only 29% of participants were probably highly infectious (produced culture-positive aerosols <5μm at ~6 days after symptom onset). These data, which comprehensively confirm variant-specific culturable SARS-CoV-2 in aerosol, inform the targeting of transmission-related interventions and public health containment strategies emphasizing improved ventilation.
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Project description:The aim of this study was to measure the immune response of alveolar macrophages (AMs) from BCG-vaccinated mice to intracellular Mtb infection in vivo. We characterized the transcriptional profile of murine Mtb-infected AMs after aerosol infection by sorting cells from bronchoalveolar lavage fluid and performing low-input RNA-sequencing.
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Project description:Since besides mucosal adaptive immunity, respiratory delivery of AdHu5Ag85A vaccine in experimental animals induced a trained phenotype in airway macrophages, we examined whether aerosol vaccination with AdHu5Ag85A could also alter the immune property of human alveolar macrophages (AM). To this end, we elected to examine the transcriptomics of BALF cells obtained from 5 participants before (wk0) and after (wk8) 1x106PFU AdHu5Ag85A aerosol vaccination. Before RNA isolation, the cells, upon revival from frozen stock, were enriched for AM and cultured with or without stimulation with M.tb lysates and transcriptionally profiled by RNAseq analysis. Principal component analysis (PCA) revealed that unstimulated (US) and stimulated (S) AM populations were separated away from each other. We then identified the differentially expressed genes (DEGs) by comparing wk0- and wk8-stimulated AM with respective unstimulated AM. By this pairwise analysis, we identified 194 and 426 genes uniquely upregulated and downregulated, respectively, in stimulated AM from aerosol vaccinated participants. The uniquely up-regulated genes in stimulated wk8 aerosol AM showed enrichment in a number of biological processes including response to anoxia (OXTR, CTGF), inflammatory response to antigenic stimuli (IL2RA, IL1B, IL20RB), tyrosine phosphorylation of STAT protein (IFNG, F2R, OSM), regulation of IL-10 production (CD83, IRF4, IL20RB, IDO1), response to IL-1 (RIPK2, SRC, IRAK2, IL1R1, XYLT1, RELA) and histone demethylation (KDM6B, KDM5B, KDM1A, KDM7A, JMJD6). In comparison, the uniquely down-regulated genes in wk8 aerosol AM did not appear significantly enriched for any biological processes. These data suggest that aerosol vaccination leads to persisting transcriptional changes in airway-resident alveolar macrophages poised for defense responses.
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