GEO DataSets

(Submitter supplied) We have developed a novel approach named LiRIP-seq to profile the global RNA-RNA interactome in Salmonella enterica. By pulse expressing T4 RNA ligase from an inducible pBAD promoter, LiRIP-seq enables in vivo proximity ligation of Hfq-bound RNAs to their interaction partners. This is followed by enrichment of ligation products (RNA chimeras) using Hfq-coIP and subsequent RNA-seq analysis.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platform:

GPL28338

20 Samples

Download data: TXT

(Submitter supplied) Longitudinal analysis of Salmonella typhimurium mRNA from superspeader mouse cecal content and stool compared to in vitro Salmonella typhimurium mRNA.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28338

27 Samples

Download data: XLS

(Submitter supplied) Antisense oligomers (ASOs) such as peptide nucleic acids (PNAs), designed to inhibit the translation of essential bacterial genes, have emerged as attractive sequence- and species-specific programmable RNA antibiotics. Yet, potential drawbacks include unwanted side effects caused by their binding to transcripts other than the intended target. To facilitate the design of PNAs with minimal off-target effects, we developed MASON (Make AntiSense Oligomers Now), a webserver for the design of PNAs that target bacterial mRNAs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

28 Samples

Download data: CSV

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

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) To screen the potential targets of Salmonella 3’ UTR derived sRNA FadZ, we compared global mRNA profiles in FadZ-deficient and -pulse expressed strains. The 40-nt FadZ sequences was cloned onto a plasmid downstream of the pBAD promoter and expression was induced by L-arabinose for 10-min in LB broth. Transcriptomic profiles were compared with strain carrying the empty control plasmid.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31144

4 Samples

Download data: TXT

(Submitter supplied) To unfold the potential links between Salmonella fatty acid oxidation and other metabolic pathways, we performed RNA-seq to draw the transcriptomic response of Salmonella in response to oleci acid treatment. We compared samples of oleic acid shock (Group OAS) and oleic acid growth (Group OAG) to glucose growth (Group GLU).

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31144

6 Samples

Download data: TXT

(Submitter supplied) We have used the RIL-seq technique to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platform:

GPL20056

4 Samples

Download data: TXT

(Submitter supplied) ProQ has become a paradigm for the emerging family of FinO domain-containing RNA binding proteins. ProQ in Salmonella enterica has been shown to act as a global RNA binding protein as it interacts with a plethora of sRNAs and mRNAs. However, little was known about processes ProQ regulates in Salmonella which have precluded to functionally characterize ProQ in vivo. In here, we show that ProQ represses the utilization of succinate as carbon source. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platforms:

GPL22775 GPL20056

24 Samples

Download data: WIG, XLSX

(Submitter supplied) IP (as previously described Chao et al., 2012; Smirnov et al., 2016) of ProQ-3xFLAG and FinO-3xFLAG in Salmonella SL1344 at different growth conditions.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platform:

GPL20056

24 Samples

Download data: WIG

(Submitter supplied) In this study we take an integrative approach to capturing targets of the Hfq- associated sRNA PinT, a known post-transcriptional timer of the two major virulence programs of Salmonella enterica, using MS2 affinity purification and RNA- sequencing (MAPS).

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20056 GPL20064

15 Samples

Download data: WIG

(Submitter supplied) Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of characterization in microbes other than Escherichia coli. Here, we have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

4 Samples

Download data: TXT, XLSX

(Submitter supplied) Small proteins are an emerging class of gene products with diverse roles in bacterial physiology. However, a full understanding of their importance has been hampered by insufficient genome annotations and a lack of characterization in microbes other than Escherichia coli. Here, we have taken an integrative approach to accelerate the discovery of small proteins and their putative virulence-associated functions in Salmonella Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platform:

GPL22775

4 Samples

Download data: CSV

(Submitter supplied) Our study highlights the power of interpreting available “omics” datasets with a focus on small proteins, and may serve as a blueprint for a data integration-based survey of small proteins in diverse bacteria.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20056

6 Samples

Download data: BW

(Submitter supplied) RcsB is a transcriptional regulator that controls expression of numerous genes in Enterobacteriaceae. RcsB accomplishes this role alone or in combination with auxiliary transcriptional factors independently or dependently of phosphorylation. To understand the mechanisms by which RcsB regulates such a large number of genes, we performed structural and in vitro and in vivo functional studies with different RcsB variants. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27045

24 Samples

Download data: TSV

(Submitter supplied) coIP-seq of FopA in Salmonella enterica Typhimurium SL1344

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platform:

GPL20056

2 Samples

Download data: WIG

(Submitter supplied) The Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect of rewiring the Fis regulatory network in Salmonella by moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the Right macrodomain of the chromosome, creating the strain GX. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

12 Samples

Download data: BW, XLSX

(Submitter supplied) The Fis nucleoid-associated protein controls the expression of a large and diverse regulon of genes in Gram-negative bacteria. Fis production is normally maximal in bacteria during the early exponential phase of batch culture growth, becoming almost undetectable by the onset of stationary phase. We tested the effect of rewiring the Fis regulatory network in Salmonella by moving the complete fis gene from its usual location near the origin of chromosomal replication to the position normally occupied by the dps gene in the Right macrodomain of the chromosome, creating the strain GX. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20056

9 Samples

Download data: BW, XLSX

(Submitter supplied) Bacteria respond to changes in their environment with specific transcriptional programmes, but even within genetically identical populations these programmes are not homogenously expressed. Such transcriptional heterogeneity between individual bacteria allows genetically clonal communities to develop a complex array of phenotypes, examples of which include persisters that resist antibiotic treatment and metabolically specialized cells that emerge under nutrient-limiting conditions. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28338 GPL23999

149 Samples

Download data: CSV

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20056

21 Samples

Download data: BW

(Submitter supplied) A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative non-ribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Bacteroides thetaiotaomicron VPI-5482

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20056 GPL28278

40 Samples

Download data: CSV, WIG