GEO DataSets

(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) 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:

GPL17070 GPL14548

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:

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) This SuperSeries is composed of the SubSeries listed below.

Organism:

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

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) 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) 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) 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) 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) 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) Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading organism with respect to global bacterial protein-protein networks. However, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ~85% of all E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

22 Samples

Download data: WIG

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

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL23797

28 Samples

Download data: WIG

(Submitter supplied) RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. more...

Organism:

Streptococcus pneumoniae

Type:

Other

Platform:

GPL23797

6 Samples

Download data: WIG

(Submitter supplied) RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. more...

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23797

22 Samples

Download data: WIG

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

Organism:

Neisseria meningitidis 8013

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24628

10 Samples

Download data: WIG

(Submitter supplied) In this study the RNA targetome of the RNA-binding protein ProQ was determined in Neisseria meninigitidis serogroup C strain 8013 by RNA-seq.

Organism:

Neisseria meningitidis 8013

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24628

6 Samples

Download data: WIG

(Submitter supplied) In this study binding sites for the RNA-binding protein ProQ was determined in Neisseria meninigitidis serogroup C strain 8013

Organism:

Neisseria meningitidis 8013

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24628

4 Samples

Download data: WIG

(Submitter supplied) Bacteria possess many small noncoding RNAs whose regulatory roles in pathogenesis are little understood due to a paucity of macroscopic phenotypes in standard virulence assays. Here, we use a novel Dual RNA-seq approach for a single-step simultaneous RNA profiling in both pathogen and host to reveal molecular phenotypes of sRNAs during infection with Salmonella Typhimurium. We identify a new PhoP/Q-activated small RNA which upon bacterial internalization acts to temporally control the expression of both, invasion-associated effectors and virulence genes required for intracellular survival. more...

Organism:

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

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20050 GPL20051

42 Samples

Download data: CSV