GEO DataSets

(Submitter supplied) Neisseria meningitidis is a human commensal that occasionally causes life-threatening infections such as bacterial meningitis and septicemia. Despite experimental evidence that gene regulation as well as the expression of small non-coding RNAs (sRNAs) affect meningococcal virulence, the organization of its transcriptome, including in particular the biogenesis of sRNAs and their mode of action, is only poorly understood. more...

Organism:

Neisseria meningitidis 8013

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL22295 GPL22296

8 Samples

Download data: WIG

(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) RNA-based regulation of gene expression is substantially contributing to the ability of bacteria to rapidly adapt to changing environmental conditions. This study employs RNAseq to define the transcriptome of Caulobacter in response to treatment with the DNA-crosslinking agent mitomycin C. We identify a small, regulatory RNA ChvR synthesized under the control of the conserved ChvIG two-component system which represses production of a TonB-dependent receptor, ChvT, in Caulobacter crescentus. more...

Organism:

Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21317

6 Samples

Download data: WIG

(Submitter supplied) The Gram-positive bacterium Clostridium difficile, a leading cause of antibiotic-associated pseudomembranous colitis, has received increasing attention due to a rising incidence of clinical C. difficile infections (CDI). Despite progress understanding bacterial factors that promote CDI-associated morbidity and mortality, many fundamental aspects of C. difficile biology remain to be explored. Compared to other Gram-positive pathogens, little is known about the bacterium’s transcriptome architecture and in particular mechanisms of post-transcriptional control. more...

Organism:

Clostridioides difficile 630

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL28932

39 Samples

Download data: WIG

(Submitter supplied) In Neisseria meningitidis iron responsive gene regulation is mediated primarily by the Ferric Uptake Regulator (Fur) protein. When complexed with iron, Fur represses gene expression by preventing transcription initiation. Fur can also indirectly activate gene expression via the repression of regulatory small RNAs (sRNA). One such Fur-and iron-regulated sRNA, NrrF, was previously identified in N. meningitidis and shown to repress expression of the sdhA and sdhC genes encoding subunits of the succinate dehydrogenase complex. more...

Organism:

Neisseria meningitidis MC58

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL10038

18 Samples

Download data: PAIR

(Submitter supplied) We report the identification of new noncoding RNAs in Brucella suis 1330 and that are associated to the chaperone protein Hfq

Organism:

Brucella suis 1330

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20974

2 Samples

Download data: GR

(Submitter supplied) We present the first genome-wide identification and characterizaion of 422 novel sRNAs in R. capsulatus. In addition we report a comparative analysis of conserved sRNAs across 24 bacterial species.

Organism:

Rhodobacter capsulatus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20771

2 Samples

Download data: XLS

(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) Stenotrophomonas maltophilia is an important opportunistic pathogen affecting primarily hospitalized and immuno-compromised hosts. We constructed an hfq deletion mutant (Delta-hfq) of S. maltophilia, and compared the behaviour of wild-type and Delta-hfq S. maltophilia cells in a variety of assays. Differential RNA sequencing analysis (dRNA-seq) of RNA isolated from S. maltophilia wild-type and Delta-hfq strains showed that Hfq regulates expression of genes encoding flagellar and fimbrial components, transmembrane proteins, as well as enzymes involved in different metabolic pathways. more...

Organism:

Stenotrophomonas maltophilia

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15858

4 Samples

Download data: WIG

(Submitter supplied) Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19729

8 Samples

Download data: WIG

(Submitter supplied) Differences in the transcriptional profile of the menigococcal strains MC58 and α710 were compared upon growth in PPM+ and on exposure to human saliva, whole blood and cerebrospinal fluid

Organism:

Neisseria meningitidis

Type:

Expression profiling by array

Platform:

GPL8787

24 Samples

Download data: GPR

(Submitter supplied) Neisseria meningitidis, a commensal β-proteobacterium of the human nasopharynx, constitutes a worldwide leading cause of sepsis and epidemic meningitis. The molecular basis for their "accidental" pathogenicity is still not fully understood. Here, we show that knock-out strains lacking the Cas9 protein are impaired in the adhesion to human nasopharyngeal cells which constitutes a central step in the pathogenesis of invasive meningococcal disease. more...

Organism:

Neisseria meningitidis 8013

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24628

8 Samples

Download data: WIG

(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) In bacteria and archaea, CRISPR loci confer adaptive, sequence-based immunity against viruses and plasmids. CRISPR interference is specified by CRISPR RNAs (crRNAs) that are transcribed and processed from CRISPR spacers and repeats. Pre-crRNA processing is essential for CRISPR interference in all systems studied thus far. Here we examine crRNA biogenesis and CRISPR interference in naturally competent Neisseria spp., including the human pathogen N. more...

Organism:

Neisseria lactamica 020-06

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16715

2 Samples

Download data: TXT

(Submitter supplied) We used the RNA-seq technology to do a genome-wide transcriptional analysis of A. pleuropneumoniae strain JL03 and investigated the transcriptome structure at a single-nucleotide resolution.The RNA-Seq based transcriptome map validated annotated genes and corrected annotations of open reading frames in the genome, and led to the identification of many functional elements (e.g. regions encoding novel proteins, non-coding sRNAs and operon structures).

Organism:

Actinobacillus pleuropneumoniae serovar 3 str. JL03

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20603

1 Sample

Download data: BED

(Submitter supplied) Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions.

Organism:

Agrobacterium tumefaciens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18897

8 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

Download data