GEO DataSets

(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) 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 Typhimurium; Salmonella enterica subsp. enterica serovar Typhi

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:

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

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:

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

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 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

(Submitter supplied) Polyamines, crucial molecules involved in cell proliferation and growth, play a pivotal role in cancer development and progression. Within the tumor microenvironment, macrophages, key components of the immune system, exhibit a complex relationship with polyamines. Evidence suggests that polyamines can modulate macrophage polarization, influencing their functional phenotypes. Here, we detected the gene DNA methylation changes in spermine-stimulated human macrophages isolated from PBMCs and TAMs.

Organism:

Campylobacter jejuni; Francisella tularensis subsp. novicida; Yersinia pestis; Staphylococcus aureus; Mycobacterium avium subsp. paratuberculosis; Cowpox virus; Escherichia coli O157:H7; Francisella tularensis subsp. mediasiatica; Paslahepevirus balayani; Yersinia pseudotuberculosis; Rickettsia prowazekii; Bartonella quintana; Mycobacterium avium; Homo sapiens; Streptobacillus moniliformis; Bartonella henselae; Francisella tularensis subsp. tularensis; Francisella tularensis subsp. holarctica; Yersinia enterocolitica; Toxoplasma gondii; Salmonella enterica subsp. enterica serovar Typhimurium; Mammarenavirus choriomeningitidis; Orthohantavirus puumalaense; Leptospira interrogans; Rickettsia typhi; Mycobacterium tuberculosis variant bovis; Mycobacterium tuberculosis; Mycobacterium tuberculosis variant microti; Mycobacterium canetti; Orthohantavirus seoulense

Type:

Methylation profiling by array

Platform:

GPL21445

4 Samples

Download data: IDAT, TXT

(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:

GPL34454 GPL570

36 Samples

Download data: CEL

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

Organism:

Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

Type:

Other

4 related Platforms

279 Samples

Download data

(Submitter supplied) Salmonella enterica is comprised of genetically distinct “serovars”, that together provide an intriguing model for exploring the genetic basis of pathogen evolution. While the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

Type:

Other

4 related Platforms

48 Samples

Download data: CSV