GEO DataSets

(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 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

(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) Characterization of bacterial behavior in the microgravity environment of spaceflight is of importance towards risk assessment and prevention of infectious disease during long-term missions. Further, this research field unveils new insights into connections between low fluid-shear regions encountered by pathogens during their natural infection process in vivo, and bacterial virulence. This study is the first to characterize the global transcriptomic and proteomic response of an opportunistic pathogen that is actually found in the space habitat, Pseudomonas aeruginosa. more...

Organism:

Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Platform:

GPL84

8 Samples

Download data: CEL

(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:

GPL20051 GPL20056

42 Samples

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(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) Hfq is a bacterial Sm-like protein which serves as a post-transcriptional regulator of global gene expression. It has been shown to be involved in a wide range of cellular processes and pathways. To characterize the regulation roles of Hfq in Brucella melitensis, the in vitro hfq induction conditions simulating intracellular environments were firstly defined, and then, the transcriptome of the hfq mutant was compared to that of the wild type strain. more...

Organism:

Brucella melitensis bv. 1 str. 16M; Brucella melitensis

Type:

Expression profiling by array

Platform:

GPL11117

4 Samples

Download data: GPR

(Submitter supplied) Salmonella enterica var. Typhimurium (S. Typhimurium) is a Gram-negative, facultative intracellular pathogen that infects the intestinal tracts of humans and animals. In the host, S. Typhimurium encounters a wide range of oxygen concentrations going from oxic conditions in the stomach to near anoxic conditions in the distal sigmoid colon-rectal junction. In Escherichia coli, FNR (Fumarate Nitrate Reductase) is one of the main regulatory proteins involved in oxygen sensing and in controlling the transcription of the genes required for the aerobic/anaerobic transition.. more...

Organism:

Salmonella; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL1835

6 Samples

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(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) Salmonella transcription profiles were obtained from samples flown on space shuttle mission STS-115, and compared to profiles from Salmonella grown under identical conditions on the ground. Keywords: stress response, transcriptional profile

Organism:

Salmonella enterica

Type:

Expression profiling by array

Platforms:

GPL6868 GPL4805

24 Samples

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(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

(Submitter supplied) Hfq is an RNA chaperone, which functions as a pleiotropic regulator for RNA metabolism in bacteria. To characterize the role of Hfq in pathogenicity of Neisseria gonorrhoeae we generated a N. gonorrhoeae hfq mutant, MS11hfq.Transcriptional analysis using a custom-made N. gonorrhoeae microarray revealed that 369 open reading frames were differentially regulated in MS11hfq compared to the wild-type (wt) strain (202 were upregulated, 167 were downregulated). more...

Organism:

Neisseria gonorrhoeae

Type:

Expression profiling by array

Platform:

GPL7101

6 Samples

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(Submitter supplied) Comparisons of overexpression of PreA (in wt or preAB mutant Salmonella) to Salmonella lacking preA or preAB in late log phase growth in LB

Organism:

Salmonella enterica; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by array

Platform:

GPL3788

12 Samples

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(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) Transcriptional profiling of K. pneumoniae comparing the wild type strain (S5) with a hfq deletion mutant (H0201). Goal was to determine the effects of Hfq absence on global K. pneumoniae gene expression.

Organism:

Klebsiella pneumoniae; Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044

Type:

Expression profiling by array

Platform:

GPL13638

1 Sample

Download data: TXT, XLS

(Submitter supplied) The alpha-proteobacterium Caulobacter crescentus thrives in oligotrophic environments and is able to optimally exploit minimal resources by entertaining an intricate network of gene expression control mechanisms. Numerous transcriptional activators and repressors have been reported to contribute to these processes, but only few studies have focused on regulation at the post-transcriptional level in C. more...

Organism:

Caulobacter vibrioides

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24555

2 Samples

Download data: XLSX