GEO DataSets

(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; Klebsiella pneumoniae; Enterobacter cloacae; Escherichia coli; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other

8 related Platforms

13 Samples

Download data: TXT, XLSX

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL17070 GPL21220

132 Samples

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(Submitter supplied) RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA-binding proteins (RBPs) are known to be involved in post-transcriptional regulation, but their global impact on RNA half-lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

120 Samples

Download data: CSV

(Submitter supplied) Plasmid maintenance costs to bacterial hosts is closely linked to the mechanisms that underlie plasmid fitness and how these costs are resolved. Herein, we performed multiple (63) serial passage to explore the compensatory mechanisms of co-evolution of multidrug-resistant IncHI2 plasmid pJXP9 and S. Typhimurium strain ATCC 14028 with or without antibiotic selection. pJXP9 could be maintained at for hundreds of generations even without drug exposure. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

8 Samples

Download data: TXT

(Submitter supplied) We report the effect of dephostatin treatment on the Salmonella transcriptome. High-throughput sequencing was used to quantify transcript levels under different growth conditions.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

12 Samples

Download data: TXT

(Submitter supplied) Movement of food-borne pathogens on moist surfaces enables them to migrate towards more favorable niches and facilitate their survival for extended periods of time. Salmonella enterica serovar Typhimurium mutants defective in OPG synthesis are unable to exhibit motility on moist surfaces (swarming) however their mobility in liquid (swim motility) remains unaffected. In order to understand the role of OPG in swarm motility, transcriptomic analysis was performed using cells growing on a moist agar surface. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18823 GPL17070

9 Samples

Download data: TXT

(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to RNA stability in Salmonella during growth in LB and mLPM media

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other

Platform:

GPL17070

39 Samples

Download data: CSV

(Submitter supplied) Analysis of the contribution of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17070

32 Samples

Download data: CSV

(Submitter supplied) We generated S. Typhimurium and S. bongori strains that express SsrB (SsrB+) or not (SsrB-) in trans to evaluate the changes in gene expression upon SsrB expression. As S. bongori evolved in the absence of SsrB, this allows us to explore the evolution of gene regulation in S. Typhimurium following horizontal gene acquisition of the SsrB response regulator.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Salmonella bongori

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17070 GPL25580

12 Samples

Download data: TXT

(Submitter supplied) While many general RNA-binding proteins have been described in eukaryotes, the small RNA chaperone Hfq and the translational regulator CsrA remain the only known global RNA-associated cofactors involved in the bacterial post-transcriptional gene expression control. Here, using an RNA-seq-based analysis of the biochemically partitioned ensemble of cellular RNAs, we uncovered a large group of transcripts that interact with the RNA-binding protein ProQ in Salmonella enterica. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

20 Samples

Download data: WIG

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

Organism:

Escherichia coli; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL14548 GPL17070

24 Samples

Download data: WIG

(Submitter supplied) Bifidobacterium thermophilum RBL67 (RBL67), a human fecal isolate and promising probiotic candidate, showed antagonistic and protective effects against Salmonella and Listeria in vitro. However, the underlying mechanisms fostering these health-related effects remain unknown. Therefor the transcriptome response of RBL67 and Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) in co-culture compared to the response in their respective mono-cultures. more...

Organism:

Bifidobacterium thermophilum; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17070 GPL19749

12 Samples

Download data: XLSX

(Submitter supplied) The alternative subunit of RNA polymerase RpoS/σS controls a global adaptive response allowing many Gram-negative bacteria to survive nutrient deprivation and various stresses and contributes to biofilm formation and virulence of Salmonella enterica serovar Typhimurium. We have addressed an important but poorly understood aspect of σS-dependent control; that of a repressor. The general assumption is that negative regulation of gene expression by σS is mainly a passive phenomenon, due to competition between σS and other sigma factors for binding to a limited amount of core RNA polymerase (RNAP). more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17070

9 Samples

Download data: XLS