GEO DataSets

(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) 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:

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

Type:

Expression profiling by array

Platforms:

GPL570 GPL34454

36 Samples

Download data: CEL

(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:

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

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) 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 Typhi str. Ty2; Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

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; Pseudomonas putida; Yersinia pseudotuberculosis; Escherichia coli K-12

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) 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) Flagella-driven motility of Salmonella enterica serovar Typhimurium facilitates host colonization. However, the large extracellular flagellum is also a prime target for the immune system. As consequence, expression of flagella is bistable within a population of Salmonella, resulting in flagellated and non-flagellated subpopulations. This allows the bacteria to maximize fitness in hostile environments. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22503

8 Samples

Download data: TXT

(Submitter supplied) Purpose: Members of the broadly distributed Rid/YER057c/UK114 protein family have imine/enamine deaminase activity, notably on a 2-aminoacrylate (2AA). Strains of Salmonella enterica, and other organisms lacking RidA, have diverse growth phenotypes, attributed to the accumulation of 2AA. The goal of this study was to use transcriptional differences between S. enterica wild-type and ridA strains to explore the breadth of the cellular consequences that resulted from accumulation of 2AA. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23956

8 Samples

Download data: XLSX

(Submitter supplied) Fimbriae are hair-like structures present on the outer membrane of many Enterobacteriaceae and such appendages are proposed to play a significant role in the attachment of the bacteria to host cells and tissues. Salmonella enterica serovar Typhimurium has the potential to produce 13 different fimbrial types, among which type 1 fimbriae is the most common found. Expression of type 1 fimbriae is cooperatively controlled by fimZ, fimY, stm0551, fimW, and fimU within the fim gene cluster. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL22962

1 Sample

Download data: XLS

(Submitter supplied) Salmonella enterica serovar Typhimurium produces type 1 fimbriae on the outer membrane and such hair-like appendages is proposed to play a significant role in the attachment of the bacteria to host cells and tissues. S. Typhimurium cultured in static broth favors expression of type 1 fimbriae. Conversely, solid agar medium represses type 1 fimbrial expression. Production of type 1 fimbriae is cooperatively regulated by fimZ, fimY, stm0551, fimW, and fimU within the fim gene cluster. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL22962

1 Sample

Download data: TXT

(Submitter supplied) Foodborne illness from contaminated fresh produce has increased over the past decade, with the enteric human pathogen Salmonella enterica being frequently implicated in foodborne illness outbreaks associated with tomato consumption. Our previous work demonstrated that Salmonella responds to tomato cultivar differences, but knowledge of the underlying genetic responses is limited. To identify the mechanisms permitting this human pathogen-plant commodity association, a genome-wide transcriptomic analysis of Salmonella on tomato shoots and roots was conducted using an RNA-seq approach. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20934

9 Samples

Download data: CSV, DIFF

(Submitter supplied) Expression profiling on a total of 4,391 genes was conducted to identify regulated S. typhimurium genes upon exposure to subinhibitory concentrations of the MEP pathway antibiotic fosmidomycin. These results were subsequently compared to a similar gene expression analysis of subinhibitory exposures of S. typhimurium to the bactericide kanamycin

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL17664

9 Samples

Download data: GPR

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

Organism:

Salmonella enterica subsp. enterica serovar Enteritidis; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91; Salmonella enterica subsp. enterica serovar Typhimurium str. DT104; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array; Genome binding/occupancy profiling by array

Platforms:

GPL19472 GPL13609

101 Samples

Download data: GPR, TXT

(Submitter supplied) S. Typhimurium SL1344 parental strain and isogenic ΔrpoS, ΔrelAΔspoT and ΔrelAΔspoTΔrpoS strains were grown to OD600=1.0, OD600=2.3, OD600=3.0 and OD600=4.2 in Luria-Bertani medium.

Organism:

Salmonella enterica subsp. enterica serovar Enteritidis; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91; Salmonella enterica subsp. enterica serovar Typhimurium str. DT104; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL13609

35 Samples

Download data: GPR

(Submitter supplied) S. Typhimurium SL1344 parental strain and isogenic ΔrpoS, ΔdksA and ΔrelAΔspoT, ΔrelAΔspoTΔrpoS and ΔrelAΔspoTΔdksA strains were grown to OD600=1.0, OD600=2.3, OD600=3.0 and OD600=4.2 in Luria-Bertani medium.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica serovar Enteritidis; Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91; Salmonella enterica subsp. enterica serovar Typhimurium str. DT104; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL13609

30 Samples

Download data: TXT

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Salmonella enterica subsp. enterica; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10902 GPL18010

4 Samples

Download data: PAIR, TXT

(Submitter supplied) FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged FabR (IP samples) and wildtype strain (mock IP samples)

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10902

2 Samples

Download data: PAIR