GEO DataSets

(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) 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

6 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:

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

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20051

12 Samples

Download data: CSV

(Submitter supplied) The aim of the project is to identify transcriptome-wide binding sites for the global RNA-binding protein ProQ in Salmonella during intracellular-like conditions.

Organism:

Salmonella enterica

Type:

Other

Platform:

GPL27048

4 Samples

Download data: WIG

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

Organism:

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

Type:

Other

Platforms:

GPL21117 GPL20056

10 Samples

Download data: WIG

(Submitter supplied) New tools for studying bacterial transcripts at the single nucleotide level offer an unparalleled opportunity to understand the bacterial transcriptome. For the model pathogen Salmonella enterica serovar Typhimurium, it is necessary to identify the regulatory inputs for all RNA transcripts, including small RNAs (sRNAs) and coding genes. Here, we use RNA-seq to define the transcriptomes of mutants lacking 18 global regulatory systems that, among other functions, modulate the expression of the SPI1 and SPI2 Type Three secretion systems in S. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17562

28 Samples

Download data: WIG

(Submitter supplied) S. typhimurium 14028 wt, hfq and smpB were harvested from log phase LB (LBlog); (2), stationary phase LB (LBstat); (3) 4h MgM medium pH 5.0 after resuspension of LB stat culture (MgMshock); and (4) log phase MgM medium pH5.0 after 100fold dilution of an LB stat culture (MgMDil). Total RNA was extracted, cDNA labeled and hybridized to a non-redundant Salmonella whole genome PCR product ORF array.

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL6868

36 Samples

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(Submitter supplied) The Gram-negative pathogen Pasteurella multocida is responsible for many important animal diseases. While a number of P. multocida virulence factors have been identified, very little is known about how gene expression and protein production is regulated in this organism. One mechanism by which bacteria regulate transcript abundance and protein production is riboregulation, which involves the interaction of a small RNA (sRNA) with a target mRNA to alter transcript stability and/or translational efficiency. more...

Organism:

Pasteurella multocida

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31945

9 Samples

Download data: CSV

(Submitter supplied) Post-transcriptional gene regulation often involves RNA-binding proteins that modulate mRNA translation and/or stability either directly through protein-RNA interactions or indirectly by facilitating the annealing of small regulatory RNAs (sRNAs). The human pathogen Streptococcus pneumoniae D39 (pneumococcus) does not encode in its genome any homologs to RNA-binding proteins known to be involved in promoting sRNA stability and function, such as Hfq or ProQ, even though it contains genes for at least 112 sRNAs. more...

Organism:

Streptococcus pneumoniae D39

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22880

6 Samples

Download data: XLS

(Submitter supplied) We used high-throughput methods to discover the Salmonella RNAs that are targeted by the bacterial Sm-like protein, Hfq. Our generic approach, using chromosomal epitope tagging and coIP-on-chip will also be useful to identify the post-transcriptional regulons of many other RNA-binding proteins. Keywords: coIP-chip

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Other

Platform:

GPL5791

4 Samples

Download data: TXT

(Submitter supplied) The expression profile of an S. Typhimurium hfq mutant-strain was compared to the parental strain under 2 different growth conditions; early stationary phase and SPI-1 (Salmonella pathogenicity island 1) inducing condition. Keywords: Genetic modification

Organism:

Salmonella enterica

Type:

Expression profiling by array

Platform:

GPL5780

12 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) In many bacteria, the base pairing between most small regulatory RNAs (sRNAs) and their targets is facilitated by the Hfq RNA chaperone. However, recent studies have shown FinO-domain proteins also bind sRNAs. To compare the contributions of Hfq and the FinO-domain ProQ protein in Escherichia coli, we carried out RIL-seq, which allows global identification of two RNAs bound to the same protein. We detected hundreds of RNA pairs on ProQ. more...

Organism:

Escherichia coli K-12

Type:

Other

Platform:

GPL24570

56 Samples

Download data: BED, WIG

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

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium; Escherichia coli

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL14548 GPL17070

24 Samples

Download data: WIG

(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:

Escherichia coli

Type:

Other

Platform:

GPL14548

4 Samples

Download data: WIG

(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) Grad-seq of Pseudomonas aerugionosa PAO1 at OD 0.3 with and without infection with ΦKZ bacteriophage

Organism:

Pseudomonas aeruginosa PAO1; Phikzvirus phiKZ

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL23999 GPL28760

44 Samples

Download data: TDF

(Submitter supplied) The small RNAs associated with protein Hfq constitute one of the largest classes of post-transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free-standing genes. Here, deep sequencing of Hfq-bound transcripts from multiple stages of growth of Salmonella Typhimurium revealed a plethora of new small RNA species from within mRNA loci, including DapZ which overlaps with the 3’ region of the biosynthetic gene, dapB. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Other

Platform:

GPL15732

14 Samples

Download data: WIG

(Submitter supplied) To determine the targets of the small regulatory RNA DapZ in S. Typhimurium, we looked at the effect of a short pulse of DapZ over-expression on the Salmonella transcriptome, as well as a DapZ variant that lacks the GcvB-like R1 region. To achieve over-expression, the wild-type DapZ and its variant were cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by array

Platform:

GPL11416

6 Samples

Download data: TXT