GEO DataSets

(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) 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:

GPL20056 GPL22775

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:

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

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) 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) 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) 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:

GPL28278 GPL20056

40 Samples

Download data: CSV, WIG

(Submitter supplied) Here, we introduce an intestinal tissue model to study human enteric infections. Our model comprises epithelial and endothelial layers, a primary intestinal collagen scaffold, and immune cells. We use Dual RNA-seq to chart the communication amongst several different cell types at the intestinal barrier and the pathogen. The results suggest that Salmonella uses its type III secretion systems to manipulate STAT3-dependent inflammatory responses locally in the epithelial compartment. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL20056

20 Samples

Download data: TXT

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

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20056 GPL20051

42 Samples

Download data

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

24 Samples

Download data: CSV

(Submitter supplied) FinO-domain proteins such as ProQ of the model pathogen Salmonella enterica have emerged as a new class of major RNA-binding proteins in bacteria. ProQ has been shown to target hundreds of transcripts including mRNAs from many virulence regions but its role, if any, in bacterial pathogenesis has not been studied. Here, using a Dual RNA-seq approach to profile ProQ-dependent gene expression changes as Salmonella infects human cells, we reveal dysregulation of bacterial motility, chemotaxis and virulence genes which is accompanied by altered mitogen-activated protein kinase signaling in the host. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

6 Samples

Download data: CSV

(Submitter supplied) In this study binding sites for the RNA-binding protein ProQ was determined in Salmonella and Escherichia coli

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344; Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platforms:

GPL20056 GPL21117

10 Samples

Download data: WIG

(Submitter supplied) The functions of many bacterial RNA-binding proteins remain obscure due to a lack of knowledge of their cellular ligands. While well-studied cold-shock protein A (CspA) family members are induced and function at low temperature, other are highly expressed in infection-relevant conditions. Here, RNA ligand profiling of all CspA-family members linked CspC and CspE with Salmonella virulence pathways. Phenotypic assays in vitro demonstrated a crucial role for these proteins in membrane stress, motility, and biofilm formation. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20056 GPL22775 GPL19729

26 Samples

Download data: TXT, WIG

(Submitter supplied) The delineation of genes in bacteria has remained an important challenge because prokaryotic genomes are often tightly packed frequently resulting in overlapping genes. We hereby present a de novo approach called REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION) to delineate translated open reading frames (ORFs) in bacteria independent of (available) genome annotation. By deep sequencing of ribosome protected mRNA fragments (RPF) to map translating ribosomes across the entire genome, REPARATION takes advantage of the recently developed ribosome profiling (Ribo-seq) technique. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20056

4 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20056

12 Samples

Download data: WIG