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The expression profiles analysis of shigella flexneri incubated in rabbit ileum

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

ORGANISM(S): Shigella flexneri Shigella flexneri 2a str. 2457T

PROVIDER: GSE12534 | GEO | 2009/05/22

SECONDARY ACCESSION(S): PRJNA112887

REPOSITORIES: GEO

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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. an overnight culture of the wild-type strain in LB broth was harvested and resuspended in 20 ml PBS buffer and then incubated in PBS at 37 degree and in rabbit ileum for 4 hours respectively.

2010-05-18 | E-GEOD-12534 | biostudies-arrayexpress

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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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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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. The two strains were cultured in LB broth into log-phase and stationary phase respectively. Then, the total RNAs were extracted and analyzed by Nimblegen biochips.

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Project description:Shigella flexneri Genome sequencing

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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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