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Dual-transcriptome of Shigella flexneri infecting human HCT116 cells

ABSTRACT: Dual-transcriptome of Shigella flexneri infecting human HCT116 cells

PROVIDER: PRJEB76160 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13172900.fastq.gz	Fastqsanger.gz
	ERR13172901.fastq.gz	Fastqsanger.gz
	ERR13172902.fastq.gz	Fastqsanger.gz
	ERR13172903.fastq.gz	Fastqsanger.gz
	ERR13172904.fastq.gz	Fastqsanger.gz

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Dual-transcriptome of Shigella flexneri infecting human HCT116 cells

Project description:Analyse the transcriptionnal changes of human colon epithelial cells (HCT116) associated with Shigella flexneri (M90T) infection and correlated with the bacterial transcriptional program.

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miRNA profiling of human colon cells infected with the bacterium Shigella flexneri

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Transcriptomic profiling of HeLa cells infected with Shigella flexneri

Project description:We evaluated the transcriptome changes induced by infection of Hela 229 cells with Shigella flexneri. The sample set consists of a control (mock), total population of infected sample and infected sample sorted into Shigella positive and Shigella negative population.

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The expression profiles analysis of shigella flexneri incubated in rabbit ileum

Project description:To find the alterations of expression profiles of shigella flexneri, we performed DNA chip analysis and proteomic analysis at the same time.

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Dual RNA-seq of zebrafish larvae infected with Shigella sonnei

Project description:Shigella flexneri is historically regarded as the primary agent of bacillary dysentery, yet the closely-related Shigella sonnei is replacing S. flexneri, especially in developing countries. The underlying reasons for this dramatic shift are mostly unknown. Using a zebrafish (Danio rerio) model of Shigella infection, we discover that S. sonnei is more virulent than S. flexneri in vivo. Whole animal dual-RNAseq and testing of bacterial mutants suggest that S. sonnei virulence depends on its O-antigen oligosaccharide (which is unique among Shigella species). We show in vivo using zebrafish and ex vivo using human neutrophils that S. sonnei O-antigen can mediate neutrophil tolerance. Consistent with this, we demonstrate that O-antigen enables S. sonnei to resist phagolysosome acidification and promotes neutrophil cell death. Chemical inhibition or promotion of phagolysosome maturation respectively decreases and increases neutrophil control of S. sonnei and zebrafish survival. Strikingly, larvae primed with a sublethal dose of S. sonnei are protected against a secondary lethal dose of S. sonnei in an O-antigen-dependent manner, indicating that exposure to O-antigen can train the innate immune system against S. sonnei. Collectively, these findings reveal O-antigen as an important therapeutic target against bacillary dysentery, and may explain the rapidly increasing S. sonnei burden in developing countries.

2019-11-19 | GSE140544 | GEO

Transcriptional Profile of the Shigella flexneri Response to Berberine

Project description:Berberine is a natural isoquinoline alkaloid found in Chinese medicinal herbs which is active against a variety of microbial infections. To examine the potential effects of berberine on Shigella flexneri, a whole-genome DNA microarray was constructed and transcriptome analysis of the cellular responses of S.flexneri when exposed to Berberine Chloride (BC) was performed.

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Shigella flexneri

Project description:Shigella flexneri Genome sequencing

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The expression profiles analysis of a virulence plasmid-cured strain of shigella flexneri

Project description:In this study, we analyzed the expression profiles of a virulence plasmid-cured strain and wild-type strain of shigella flexneri. The results showed that the genes of glp regulon were upregulated in mutant bacteria in stationary phase cultures.

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Shigella flexneri 5a

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Expression analysis of Shigella flexneri 2a strain 301

Project description:Investigation of whole genome gene expression to identify overlooked sRNAs and sORFs. Background The completion of numerous genome sequences has introduced an era of whole-genome study. However, many real genes, including small RNAs (sRNAs) and small ORFs (sORFs), are missed in genome annotation. In order to improve genome annotation, we sought to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery or shigellosis. Results Firstly, we identified 64 sRNAs in Shigella which is experimentally validated in other bacteria based on sequence conservation. Secondly, among possible approaches to search for sRNAs, we employed computer-based and tiling array based methods, followed by RT-PCR and northern blots. This allowed us to identify 12 sRNAs in Shigella flexneri strain 301. We also find 29 candidate sORFs. Conclusions This investigation provides an updated and comprehensive annotation of the Shigella genome, increases the expected numbers of sORFs and sRNAs with the corresponding impact on future functional genomics and proteomics studies. Our method can be used for the large scale reannotation of sRNAs and sORFs in any microbe whose genome sequence is available.

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