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Dual RNA-seq – Dual RNA-seq of further sRNA mutants

ABSTRACT: Dual RNA-seq – Dual RNA-seq of further sRNA mutants

OTHER RELATED OMICS DATASETS IN: GSE67950GSE67759GSE67951GSE67757GSE67948GSE67952GSE67758

PROVIDER: PRJNA281338 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2981470.fastq.gz	Fastqsanger.gz
	SRR2981480.fastq.gz	Fastqsanger.gz
	SRR2981490.fastq.gz	Fastqsanger.gz
	SRR2981500.fastq.gz	Fastqsanger.gz
	SRR2981471.fastq.gz	Fastqsanger.gz

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Dual RNA-seq – Dual RNA-seq of further sRNA mutants

Project description:Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity is shown to adjust the human response to replicating Salmonella, and have a pervasive impact on host RNA expression both inside and outside protein-coding regions including infection-specific alterations of an array of long noncoding RNAs. Our study provides a paradigm for a comprehensive RNA-based analysis of intracellular bacterial pathogens without their physical purification from a host and a new discovery route for hidden functions of pathogen genes.

2015-12-11 | GSE67952 | GEO

Dual RNA-seq – sRNA profiling in various cell types

Project description:Dual RNA-seq – sRNA profiling in various cell types

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Dual RNA-seq â sRNA profiling in various cell types

2015-12-11 | E-GEOD-67947 | biostudies-arrayexpress

Dual RNA-seq – Pilot Dual RNA-seq

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Dual RNA-seq – Comparative Dual RNA-seq in pig macrophages

Project description:Dual RNA-seq – Comparative Dual RNA-seq in pig macrophages

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Dual RNA-seq – High-resolution comparative Dual RNA-seq time-course

Project description:Dual RNA-seq – High-resolution comparative Dual RNA-seq time-course

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Dual RNA-Seq

Project description:Dual RNA-Seq of macrophages harbouring purA or WT Salmonella

| PRJEB41486 | ENA

Dual RNA-seq – sRNA profiling in various cell types

2015-12-11 | GSE67947 | GEO

Dual RNA-seq – rRNA depletion establishment

Project description:Dual RNA-seq – rRNA depletion establishment

| PRJNA280838 | ENA

The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin tolerant Staphylococcus aureu

Project description:Vancomycin tolerance in multidrug resistance Staphylococcus aureus is correlated with dysregulation of small RNAs although their contribution to antibiotic tolerance in poorly understood. RNA-RNA interactome profiling techniques are expanding our understanding of sRNA-mRNA interactions in bacteria; however, determining the function of these interactions for hundreds of sRNA-mRNA pairs is a major challenge. At steady-state, protein and mRNA abundances are often highly correlated and lower than expected protein abundance may indicate translational repression of an mRNA. We used label-free quantitative proteomics to examine changes in protein expression in vancomycin tolerant S. aureus strain in response to vancomycin treatment. We correlated the protein levels with gene transcript abundance and ribosome occupancy to identify sRNA-mRNA interactions that regulate mRNA translation. We used the machine learning technique self-organising maps (SOMS) to cluster genes with similar transcription and translation patterns and identified a cluster of mRNAs that appeared to be post-transcriptionally repressed. By integrating our clustering analysis with the sRNA-mRNA interactome data generated in vancomycin tolerant S. aureus by RNase III-CLASH, we identified a cluster of sRNAs that may be mediating translational repression. We have confirmed sRNA-dependant post-transcriptional repression of several mRNAs in this cluster. Two of these interactions are mediated by RsaOI, a sRNA that is highly upregulated by vancomycin, and these targets include HPr and the cell-wall autolysin Atl, with only Atl downregulated at the protein level upon vancomycin treatment. These findings suggest RsaOI coordinates carbon metabolism and cell wall turnover during vancomycin treatment

2024-03-18 | PXD049022 | Pride

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