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Shigella flexneri

ABSTRACT: Shigella flexneri Raw sequence reads

PROVIDER: PRJNA527970 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	SRR8787490_1.fastq.gz	Fastqsanger.gz
	SRR8787490_2.fastq.gz	Fastqsanger.gz
	SRR8787500_1.fastq.gz	Fastqsanger.gz
	SRR8787500_2.fastq.gz	Fastqsanger.gz
	SRR8787491_1.fastq.gz	Fastqsanger.gz

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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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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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Expression analysis of Shigella flexneri 2a strain 301

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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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