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Items: 13

1.

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

(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
Series
Accession:
GSE216013
ID:
200216013

2.

Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives

(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
Download data
Series
Accession:
GSE234010
ID:
200234010

PubMed Full text in PMC Similar studies

3.

Improved RNA stability estimation through Bayesian modeling reveals most bacterial transcripts have sub-minute half-lives [RIF-seq]

(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
Series
Accession:
GSE234009
ID:
200234009

PubMed Full text in PMC Similar studies

4.

A trade-off for maintenance of multidrug-resistance IncHI2 plasmids in Salmonella Typhimurium through co-evolution

(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
Series
Accession:
GSE197475
ID:
200197475

PubMed Full text in PMC Similar studies

5.

RNA-sequencing of dephostatin-treated Salmonella

(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
Series
Accession:
GSE147414
ID:
200147414

PubMed Similar studies SRA Run Selector

6.

Transcriptomic analysis of swarm motility phenotype of Salmonella enterica serovar Typhimurium mutant defective in periplasmic glucan synthesis

(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
Series
Accession:
GSE86311
ID:
200086311

SRA Run Selector

7.

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

(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
Series
Accession:
GSE107835
ID:
200107835

PubMed Full text in PMC Similar studies SRA Run Selector

8.

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

(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
Series
Accession:
GSE107834
ID:
200107834

PubMed Full text in PMC Similar studies SRA Run Selector

9.

RNA-sequencing of SsrB-dependent gene expression in S. Typhimurium and S. bongori

(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
Series
Accession:
GSE120043
ID:
200120043

PubMed Similar studies SRA Run Selector

10.

Fraction-wise RNA-seq of the Salmonella Typhimurium SL1344 cell lysate resolved on a 10-40% glycerol gradient

(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
Series
Accession:
GSE62986
ID:
200062986

PubMed Full text in PMC Similar studies SRA Run Selector

11.

Partitioning of a RNA interactome by gradient profiling (Grad-seq)

(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
Series
Accession:
GSE62988
ID:
200062988

PubMed Full text in PMC Similar studies

12.

Transcriptome response of Salmonella enterica subsp. enterica serovar Typhimurium N-15 and Bifidobacterium thermophilum RBL67 in co-culture

(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
Series
Accession:
GSE65716
ID:
200065716

PubMed Full text in PMC Similar studies SRA Run Selector

13.

Gene repression by sigmaS: sigma competition for binding to RNA polymerase or more?

(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
Series
Accession:
GSE46380
ID:
200046380

PubMed Full text in PMC Similar studies SRA Run Selector

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