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Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

ABSTRACT: Transcriptional profile of Salmonella enterica serovar Typhimurium 4/74 wild-type and mutants using strand-specific RNA-seq

PROVIDER: PRJNA315446 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3233300.fastq.gz	Fastqsanger.gz
	SRR3233310.fastq.gz	Fastqsanger.gz
	SRR3233320.fastq.gz	Fastqsanger.gz
	SRR3233301.fastq.gz	Fastqsanger.gz
	SRR3233311.fastq.gz	Fastqsanger.gz

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Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

Project description:Salmonella enterica serovar Typhimurium 4/74 transcriptomics using strand-specific RNA-seq

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Transcriptional profile of Salmonella enterica serovar Typhimurium 4/74 wild-type and mutants using strand-specific RNA-seq

Project description:New tools for studying bacterial transcripts at the single nucleotide level offer an unparalleled opportunity to understand the bacterial transcriptome. For the model pathogen Salmonella enterica serovar Typhimurium, it is necessary to identify the regulatory inputs for all RNA transcripts, including small RNAs (sRNAs) and coding genes. Here, we use RNA-seq to define the transcriptomes of mutants lacking 18 global regulatory systems that, among other functions, modulate the expression of the SPI1 and SPI2 Type Three secretion systems in S. Typhimurium strain 4/74. We directly compared the roles of the major regulators of transcription, and reported the effects of the regulatory mutations on expression of sRNAs. We also use this method to describe the impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts. Transcriptome analysis of S. Typhimurium 4/74 using RNA isolated wild-type and mutants grown under infection-relevant conditions.

2016-08-09 | E-GEOD-79314 | biostudies-arrayexpress

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Expression analysis of Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant

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Expression analysis of Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant

Project description:Investigation of whole genome gene expression level changes in a Salmonella enterica serovar Typhimurium UK1 delta-iacP mutant, compared to the wild-type strain. IacP is resoponsible for the secretion of virulence effector proteins via the type III secretion system, thereby contributing the virulence of S. Typhimurium. The mutants analyzed in this study are further described in Kim et al. 2011. Role of Salmonella Pathogenicity Island 1 Protein IacP in Salmonella enterica Serovar Typhimurium Pathogenesis. Infection and Immunity 79(4):1440-1450 (PMID 21263021). A chip study using total RNA recovered from two separate wild-type cultures of Salmonella enterica serovar Typhimurium UK1 and two separate cultures of a mutant strain, Salmonella enterica serovar Typhimurium UK1 delta-iacP. Each chip measures the expression level of 4,302 genes from Salmonella enterica serovar Typhimurium.

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Transcription profiling of wild type, waaG mutant and rfaH mutant Salmonella enterica serovar Enteritidis PT4 and serovar Typhimurium to investigate live-attenuated vacine candidates

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Salmonella enterica serovar Typhimurium 4/74 transcriptomics using strand-specific RNA-seq

Project description:Bacterial transcription networks typically consist of hundreds of transcription factors and thousands of promoters. However, current attempts to map bacterial promoters have failed to report the true complexity of bacterial transcription. The differential RNA-seq (dRNA-seq) approaches only identified a subset of promoters because they involved few growth conditions. Here, we present a simplified approach for global promoter identification in bacteria, based upon the analysis of RNA-seq data from multiple environmental conditions. RNA was extracted from Salmonella enterica serovar Typhimurium (S. Typhimurium) grown in 22 different environmental conditions, which were devised to reflect the pathogenic lifestyle of S. Typhimurium. Individual RNA samples were combined into two pools for sequencing. In just two runs of strand-specific RNA-seq and dRNA-seq of the pooled sample we identified 3701 promoters (Pool sample). In further experiments, we found that individual in vitro conditions stimulate the expression of about 60% of the S. Typhimurium genome, whereas the suite of 22 conditions induced expression of 87% of S. Typhimurium genes. We discovered environmental conditions that induce many genes within Salmonella pathogenicity islands and identified 78 new sRNAs. In S. Typhimurium there is now experimental evidence for 280 sRNAs, and we classified them in terms of location and Hfq-binding. Transcriptome analysis of S. Typhimurium 4/74 using RNA from 22 different conditions using RNA-seq. Also, RNA from each condition was pooled into one sample (RNA Pool). Differential RNA-seq (dRNA-seq) was performed for 5 of the samples from the 22 environmental conditions.

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