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) Polymyxin B is considered as a last-resort antibiotic for multidrug-resistant or extensively drug-resistant gram-negative bacterial infections. Addressing Salmonella resistance to polymyxin B is crucial for global public health. In this study, transcriptomic detection and analysis were used to clarify the mechanisms by which CpxA-deleted S.typhimurium is involved in resistance to polymyxin B stress, which may be related to processes such as increased assembly of bacterial flagella.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35078

6 Samples

Download data: XLS

(Submitter supplied) To study the biological function of the novel 3′ UTR-derived sRNA, ManS, originating from a S. enterica-specific genomic island, STM1127-STM1131, we conducted RNA-pulse expression combined with RNA sequencing to screen for mRNAs repressed by ManS. Additionally, we compared the transcriptomic changes between wild-type and ManS-deleted strains during N-acetylmannosamine (ManNAc) metabolism.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31144

10 Samples

Download data: TXT

(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) We present genome-wide RpoD-family sigma factors (RpoD, RpoS, and RpoH) binding profiles and transcriptome profiles in Salmonella Typhimurium 14028s under both control (37°C) and sublethal heat shock conditions (42°C). These genome-scale experimental data show how three RpoD-family sigma factors simultaneously coordinate many types of cellular processes to orchestrate the overall response of S. Typhimurium to heat stress.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28222

12 Samples

Download data: XLSX

(Submitter supplied) We present genome-wide RpoD-family sigma factors (RpoD, RpoS, and RpoH) binding profiles and transcriptome profiles in Salmonella Typhimurium 14028s under both control (37°C) and sublethal heat shock conditions (42°C). These genome-scale experimental data show how three RpoD-family sigma factors simultaneously coordinate many types of cellular processes to orchestrate the overall response of S. Typhimurium to heat stress.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28222

8 Samples

Download data: TSV

(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) Here we present high-resolution 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. ATCC 14028

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34632

22 Samples

Download data: CSV, TXT

(Submitter supplied) The non-typhoidal Salmonella enterica serotype Heidelberg is a major foodborne pathogen primarily transmitted to humans through contaminated poultry products. Current control measures emphasize novel approaches to mitigate Salmonella Heidelberg colonization in poultry and the contamination of poultry products, thereby reducing its transmission to humans. This study highlight that commensal E. coli 47-1826 can potentially be used to control of S. more...

Organism:

Escherichia coli; Salmonella enterica subsp. enterica serovar Heidelberg

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34889 GPL34890 GPL16085

9 Samples

Download data: TXT

(Submitter supplied) SdiA is a LuxR-type protein found in some Enterobacteriaceae. SdiA encoding bacteria do not encode a luxI homolog and rely on foreign bacteria for the production of N-acyl homoserine lactones (AHLs), SdiA's ligand. The regulon of Salmonella SdiA is largely unknown. In this study, we measured the sdiA dependent transcriptional changes of two serovars of Salmonella, Typhimurium and Typhi, exposed to synthetic AHLs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhi; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34830 GPL23683

24 Samples

Download data: CSV

(Submitter supplied) The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organism Escherichia coli, as well as several major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, and the E. coli Keio single-gene deletion library is often regarded as a gold standard for gene essentiality studies. more...

Organism:

Klebsiella pneumoniae; Citrobacter rodentium; Salmonella enterica subsp. enterica serovar Enteritidis; Enterobacter cloacae; Escherichia coli; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other

8 related Platforms

13 Samples

Download data: TXT, XLSX

(Submitter supplied) This study characterized the involvement of yihO and yihQ of yih operon associated with O-antigen capsule formation, in phenotypic characteristics, intracellular survival, and virulence in Salmonella Typhimurium (ST). Bacterial fitness screening of the ∆yihO, ∆yihQ, and ∆yihO/Q ST mutants showed impairment in biofilm formation, motility, starvation, and stress survival. In vitro studies using phagocytic and non-phagocytic cells revealed a significant decrease in bacterial invasion and intracellular replication, particularly by the ∆yihO and ∆yihO/Q ST which correlated with the lack of proliferation ability in vivo as observed in the liver and spleen colonization. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30218

4 Samples

Download data: XLSX

(Submitter supplied) We report the transcriptomic changes in Salmonella Typhimurium exposed to sub-lethal sonophotocatalytic disinfection. The current data suggests that more than 120 genes are significantly expressed during the process. The genes associated with the flagellar assembly were found to be significantly up-regulated during the disinfection, which may have impacts on the phenotypic attributes of the bacteria.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30455

2 Samples

Download data: XLSX

(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) Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. more...

Organism:

Serratia marcescens; Enterobacter cloacae; Escherichia coli; Klebsiella pneumoniae; Salmonella enterica; Citrobacter rodentium

Type:

Expression profiling by high throughput sequencing

6 related Platforms

64 Samples

Download data: TXT

(Submitter supplied) Purpose: Searching for sRNAs in Salmonella pullorum by RNA sequencing and exploring their functions.Methods: High-throughput sequencing of RNA extracted from Salmonella pullorum under normal growth conditions to detect newly discovered sRNAs, followed by experiments to verify their functions.Results: The proportion of Clean Reads of this sequencing was >65%, and the base Q30s were all above 85%, indicating that the sequencing quality is good and can be used for subsequent analysis. more...

Organism:

Salmonella enterica subsp. enterica serovar Pullorum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL34564

3 Samples

Download data: XLSX

(Submitter supplied) The ability of bacteria to sense and respond to mechanical forces has important implications for pathogens during the in vivo infection process, as they experience wide fluid shear fluctuations in the host. However, relatively little is known about how mechanical forces encountered in the infected host drive microbial pathogenesis. We previously demonstrated an inverse relationship between fluid shear-induced responses of classic gastrointestinal disease-causing Salmonella Typhimurium (x3339) and systemic multidrug resistant (MDR) S. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24393

6 Samples

Download data: XLSX