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

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

PROVIDER: PRJNA215033 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR951027.fastq.gz	Fastqsanger.gz
	SRR951028.fastq.gz	Fastqsanger.gz
	SRR951029.fastq.gz	Fastqsanger.gz
	SRR951030.fastq.gz	Fastqsanger.gz
	SRR951031.fastq.gz	Fastqsanger.gz

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

Project description:Intra-macrophage transcriptome of Salmonella enterica serovar Typhimurium 4/74 using strand-specific RNA-seq

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

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FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344

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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.

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

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