Pseudomonas aeruginosa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA682859 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Deeper understanding of T cell biology is crucial for the development of new therapeutics. Human naïve T cells have low RNA content and their numbers can be limiting; therefore we set out to determine the parameters for robust ultra-low input RNA sequencing. We performed transcriptome profiling at different cell inputs and compared three protocols: Switching Mechanism at 5’ End of RNA Template technology (SMART) with two different library preparation methods (Nextera (SMART_Nxt) and Clontech (SMART_CC)), and AmpliSeq technology. As the cell input decreased the number of detected coding genes decreased with SMART, while stayed constant with AmpliSeq. However, SMART enables detection of non-coding genes, which is not feasible for AmpliSeq. The detection is dependent on gene abundance, but not transcript length. The consistency between technical replicates and cell inputs was comparable across methods above 1K but highly variable at 100 cell input. Sensitivity of detection for differentially expressed genes decreased dramatically with decreased cell inputs in all protocols, support that additional approaches, such as pathway enrichment, are important for data interpretation at ultra-low input. Finally, T cell activation signature was detected at 1K cell input and above in all protocols, with AmpliSeq showing better detection at 100 cells.
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Project description:Detection of GES-5-producing multidrug-resistant Pseudomonas aeruginosa in Japan
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Project description:Detection of GES-5-producing multidrug-resistant Pseudomonas aeruginosa in Japan
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2023-06-10 | E-MTAB-12966 | biostudies-arrayexpress
Project description:Untargeted metabolomics analysis of in vitro headspace volatiles from 81 Pseudomonas aeruginosa bacterial isolates from individuals with cystic fibrosis. Headspace volatiles were collected using solid-phase microextraction (SPME) (in triplicate) and comprehensive two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS). 15 replicates of un-inoculated media were prepared and analyzed in parallel, for a total of 258 samples.
2020-05-31 | ST001414 | MetabolomicsWorkbench
Project description:Biofilms are the most common cause of bacterial infections in humans and notoriously hard to treat due to their ability to withstand antibiotics and host immune defenses. To overcome the current lack of effective antibiofilm therapies and guide future design, the identification of novel gene targets is crucial. In this regard, transcriptional regulators have been proposed as promising targets for antimicrobial drug design, since they simultaneously affect multiple genes, typically lack human orthologs, and can be inactivated by small molecules that prevent dimerization. Therefore, a Transposon insertion sequencing approach was employed to systematically identify regulatory genes phenotypically affecting biofilm growth in Pseudomonas aeruginosa PA14. A screen of a pool of 300,000 transposon insertion mutants identified 349 genes involved in biofilm growth on hydroxy apatite, including 47 regulators. Detection of 19 regulatory genes participating in well-established biofilm pathways validated the results. An additional 28 novel prospective biofilm regulators suggested the requirement of multiple one-component transcriptional regulators. Defect phenotypes were confirmed for five one-component transcriptional regulators PA14_43720, PA14_56430, PA14_36180, arsR and merD as well as the protein kinase yeaG, which have not been implicated in biofilm growth before. Promisingly, the transcriptional regulator PA14_43720 displayed a conserved role in biofilm growth since its ortholog in P. aeruginosa strain PAO1 was also required for biofilm growth. Overall, our results highlighted that the gene network driving biofilm growth is complex and involves regulators beyond the primarily studied groups of two-component systems and cyclic diguanylate signaling proteins.
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Project description:Detection of sRNAs in Pseudomonas aeruginosa
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Project description:TraDIS study to identify novel immunity proteins and their effector proteins associated with the Type VI secretion system (T6SS) in Pseudomonas aeruginosaThese data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-05-12 | E-ERAD-317 | biostudies-arrayexpress
Project description: Not available
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