GEO DataSets

(Submitter supplied) LeuO, initially identified as a leucine regulator in Escherichia coli, has since been identified as a global regulator required for bacterial pathogenicity in a broad range of bacteria, including gram-negative pathogens, such as Salmonella, Shigella, and Vibrio; and gram-positive bacteria, such as Streptococcus pneumoniae. However, the regulatory roles and targets of LeuO vary among species. In the Salmonella enterica subsp. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL33626

1 Sample

Download data: NARROWPEAK

(Submitter supplied) Salmonella enterica serovar Typhimurium (S. Typhimurium) infection triggers an inflammatory response that changes the concentration of luminal metabolites in the gut, resulting in a distinct environment from a healthy one. We recently demonstrated that S. Typhimurium possesses the ability to form biofilms within the host environment and responds to nitrate as a signaling molecule, enabling it to modulate the transition between sessile and planktonic states. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33626

6 Samples

Download data: XLSX

(Submitter supplied) Here we present high-resolution Cappable-Seq transcriptomic data on Salmonella gene expression under optimal, starvation and hydrogen peroxide conditions, and after 8 and 15 hours of co-culture with A. Castellanii.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34612

20 Samples

Download data: CSV, TXT

(Submitter supplied) We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli and Salmonella typhimurium, investigates the impact of DNA supercoiling on ParBF DNA binding profiles in vivo. We found that variation in DNA supercoiling does not significantly affect the ParB DNA binding profiles even on linear DNA.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25140 GPL34219

18 Samples

Download data: TXT

(Submitter supplied) Elongation factor P (EF-P) is required to enhance peptidyl transferase on pausing ribosomes, which can be induced by certain codons on mRNA. It regulates expression of genes in specific conditions. Therefore, to search EF-P mediated ribosome stalling motif, ribosome profiling has been used on organisms such as yeast and E. coli. However, it has not been addressed on the intracellular pathogen Salmonella Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Other

Platform:

GPL33996

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Many bacteria are often resistant to antibiotic treatment and drugs because, even if these drugs are effective, bacteria can slow down their growth rate and thus attenuate the effectiveness of the drug. A similar growth-rate control is detected in pathogenic bacteria that infect and persist inside their hosts. The bacterial growth rate within host cells can be regulated by multiple signaling pathways, most of which are still unknown. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23619

4 Samples

Download data: TSV

(Submitter supplied) Many bacteria are often resistant to antibiotic treatment and drugs because, even if these drugs are effective, bacteria can slow down their growth rate and thus attenuate the effectiveness of the drug. A similar growth-rate control is detected in pathogenic bacteria that infect and persist inside their hosts. The bacterial growth rate within host cells can be regulated by multiple signaling pathways, most of which are still unknown. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32269

4 Samples

Download data: BEDGRAPH

(Submitter supplied) The deposited microarray data were generated in a study that integrated the gene expression profiles and metabolic responses of Caco2 cells incubated with Bifidobacterium infantis subsp. infantis and Salmonella enterica subsp. enterica sv. Typhimurium. The aim of this study was to investigate the interaction of B. infantis, S. Typhimurium, and host cells (Caco2) in the course of infection to understand the molecular mechanics of probiotic-pathogen-host interactions.

Organism:

Homo sapiens; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platforms:

GPL570 GPL34454

36 Samples

Download data: CEL

(Submitter supplied) An ex vivo system was developed to monitor Salmonella growth, virulence (SPI1 expression) and gene expression (measured by microarray) in response to the permissive and exclusive communities. Yellow fluorescent protein (yfp) and cyan fluorescent protein (cfp) variants were fused to the rrn growth-dependent promoter and the hilA operon (SPI-1 cell invasion locus), respectively, in Salmonella. Fluorescence associated with the YFP and CFP reporters was used to monitor Salmonella growth and SPI1 virulence gene expression in co-culture with cecal communities ex vivo. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL14855

11 Samples

Download data: XYS

(Submitter supplied) RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22503

2 Samples

Download data: GFF, TXT

(Submitter supplied) RpoD is a houskeeping sigma factor and RpoN is an alternative one. It was identified their intragenic and intergenic binding sites and association with the RNA polymerase.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17439 GPL22503

8 Samples

Download data: GFF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL17439 GPL22503

10 Samples

Download data: GFF

(Submitter supplied) Flagellum plays a crucial role in the invasion process of Salmonella, while also functioning as a significant antigen to trigger host pyroptosis. The regulation of flagella biogenesis is essential for both pathogenicity and immune escape of Salmonella. Here, we identified the conserved and unknown function protein STM0435 as a new flagellar regulator. ∆stm0435 strain exhibit higher pathogenicity in both cellular and animal infection experiments compared to wild-type Salmonella. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33626

6 Samples

Download data: TXT

(Submitter supplied) We report the findings of genes under the transcriptional control of Gre factors by comparing RNA-seq data from parental, wild-type Salmonella enterica enterica Typhimurium 14028s and a ∆greA ∆greB strain. By comparing differential gene expression, we identify a metabolic scheme for responding to oxidative stress that is regulated in part by the action of Gre factors

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32269

16 Samples

Download data: CSV

(Submitter supplied) Salmonella enterica represent a major disease burden worldwide. While non-typhoidal Salmonella (NTS) serovars trigger self-limiting diarrhoea, leading to occasional secondary bacteraemia, S. enterica serovar Typhi is responsible for potentially life-threatening Typhoid fever. Dendritic cells (DCs) are key professional antigen presenting cells of the human immune system. The ability of pathogenic bacteria to subvert DC functions and prevent T cell recognition contributes to their survival and dissemination within the host. more...

Organism:

Homo sapiens; Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580; Salmonella enterica subsp. enterica serovar Typhi str. Ty2

Type:

Expression profiling by high throughput sequencing

7 related Platforms

93 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli; Klebsiella pneumoniae; Shigella flexneri; Staphylococcus aureus; Escherichia coli K-12; Pseudomonas putida; Yersinia pseudotuberculosis

Type:

Genome binding/occupancy profiling by high throughput sequencing

9 related Platforms

102 Samples

Download data: GFF

(Submitter supplied) Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22503

6 Samples

Download data: GFF

(Submitter supplied) DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24956

4 Samples

Download data: DIFF

(Submitter supplied) Salmonella Typhimurium is one of the major foodborne pathogens due to its biofilm formation on food contact surfaces. A polymer of positively charged lysine, ε-Polylysine has been demonstrated to inhibit biofilm formation of both Gram-positive and -negative bacteria. To elucidate the mechanism for inhibition of biofilm formation by ε-Polylysine, transcriptional profiles were compared between the cells before and after treatment with ε-Polylysine in Salmonella Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL27746

9 Samples

Download data: TXT

(Submitter supplied) A set of genes are differentially regulated in the presence of extra copy of the mgtC gene. Provide a hint of potental target of the MgtC protein.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23619

4 Samples

Download data: TXT