Shigella flexneri 2a strain:2a
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ABSTRACT:
PROVIDER: PRJNA379672 | ENA |
REPOSITORIES: ENA
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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.
2011-06-27 | GSE22800 | GEO
Project description:Shigella flexneri 2a strain:serotype 2a Assembly
| PRJNA789735 | ENA
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. Study using total RNA recovered from five conditions.
2011-06-27 | E-GEOD-22800 | biostudies-arrayexpress
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.
2008-12-22 | GSE12535 | GEO
Project description:Whole genome sequencing of Shigella flexneri serotype 2a, an opportunistic pathogen
| PRJDB2601 | ENA
Project description:Expression analysis of Shigella flexneri 2a strain 301
| PRJNA127803 | ENA
Project description:Shigella flexneri 2a str. 301 resequencing
| PRJNA383762 | ENA
Project description:Shigella flexneri 2a str. 2457T genome sequencing project
| PRJNA48255 | ENA
Project description:Shigella flexneri 2a str. 2457T Raw sequence reads
| PRJNA328875 | ENA
Project description:Shigella flexneri 2a str. 301 Raw sequence reads
| PRJNA360708 | ENA