GEO DataSets

(Submitter supplied) Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging human pathogen causing invasive infection in immune-competent hosts. The hypervirulence is strongly linked to the overproduction of hypermucovisous capsule, but the underlining regulatory mechanism of hypermucoviscosity (HMV) has been elusive, especially at the post-transcriptional level mediated by small RNAs (sRNAs). Using a recently developed RNA interactome profiling approach, we have investigated the Hfq-associated sRNA regulatory network and established the first in vivo RNA-RNA interactome in HvKP. more...

Organism:

Klebsiella pneumoniae subsp. pneumoniae ATCC 43816

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33764

14 Samples

Download data: TXT

(Submitter supplied) To map the Hfq-mediated RNA regulatory network in HvKP, we harnessed the LiRIP-seq approach recently established in our lab, which enabled global profiling of RNA-RNA interactomes in live bacteria. Transformation of the pBAD-t4rnl1 plasmid into Klebsiella allowed us to express T4 RNA ligase 1 for proximity-ligation of RNAs in vivo, followed by co-immunoprecipitation (coIP) to enrich the Hfq-bound RNA transcripts (singleton reads) and ligated RNA fragments (chimeras: sRNA-mRNA, sRNA-sRNA, etc).

Organism:

Klebsiella pneumoniae subsp. pneumoniae ATCC 43816

Type:

Other

Platform:

GPL33764

6 Samples

Download data: TXT

(Submitter supplied) Conjugative plasmids are the main vehicle for the horizontal spread of antimicrobial resistance (AMR). Although AMR plasmids provide advantages to their hosts under antibiotic pressure, they can also disrupt the cell’s regulatory network, impacting the fitness of their hosts. Despite the importance of plasmid-bacteria interactions on the evolution of AMR, the effects of plasmid carriage on host physiology has remained underexplored, and most studies have focused on model bacteria and plasmids that lack clinical relevance. more...

Organism:

Citrobacter freundii; Klebsiella pneumoniae; Klebsiella variicola; Escherichia coli

Type:

Expression profiling by high throughput sequencing

6 related Platforms

78 Samples

Download data: TSV

(Submitter supplied) Plasmids are extrachromosomal genetic elements commonly found in bacteria. Plasmids are known to fuel bacterial evolution through horizontal gene transfer (HGT), but recent analyses indicate that they can also promote intragenomic adaptations. However, the role of plasmids as catalysts of bacterial evolution beyond HGT remains poorly explored. In this study, we investigate the impact of a widespread conjugative plasmid, pOXA-48, on the evolution of various multidrug-resistant clinical enterobacteria. more...

Organism:

Citrobacter freundii; Klebsiella pneumoniae; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25368 GPL34185 GPL28669

55 Samples

Download data: TSV

(Submitter supplied) Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcomeovercame these hurdles through the development of “Ribo-FilterOut”, which is based on the separation of footprints from ribosome subunits by ultrafiltration, and “Ribo-Calibration”, which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. more...

Organism:

Saccharomyces cerevisiae; Drosophila melanogaster; Escherichia coli; Arabidopsis thaliana; Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

9 related Platforms

114 Samples

Download data: CSV, TXT

(Submitter supplied) We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) of the DNA binding pattern of ParBF (SopB) of plasmid F. This study, performed in E. coli and Salmonella typhimurium, investigates the impact of DNA supercoiling on ParBF DNA binding profiles in vivo. We found that variation in DNA supercoiling does not significantly affect the ParB DNA binding profiles even on linear DNA.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. LT2; Escherichia coli

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL25140 GPL34219

18 Samples

Download data: TXT

(Submitter supplied) Elongation factor P (EF-P) is required to enhance peptidyl transferase on pausing ribosomes, which can be induced by certain codons on mRNA. It regulates expression of genes in specific conditions. Therefore, to search EF-P mediated ribosome stalling motif, ribosome profiling has been used on organisms such as yeast and E. coli. However, it has not been addressed on the intracellular pathogen Salmonella Typhimurium. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Other

Platform:

GPL33996

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Comparison of RNA expression profiles from STEC strain FHI96 expressing methyltransferase mod (ON; 52reps) or not (OFF; 51reps).

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: TXT

(Submitter supplied) Cronobacter (C.) is an important emerging opportunistic foodborne pathogen representing significant cause of mortality in neonatal patients with bacteremia and meningitis. Knowledge on the pathobiology of Cronobacter mediated meningitis has to a large extend been explored using in vitro models. To explore the innate immune response against the neonatal sepsis/meningitis causing isolate C. turicensis z3032 in vivo, zebrafish larvae (Danio rerio) were used as infection model. more...

Organism:

Cronobacter turicensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33542

2 Samples

Download data: CSV

(Submitter supplied) We examined the DNA damage response of bacterium E. coli using the replication inhibitor azidothyimdine (AZT), and RNA-Seq analysis. We confirm the induction of classic SOS loci by AZT and identify several genes, including many of the pyrimidine pathway, that are induced dependent on LexA cleavage, but have not been previously demonstrated to be DNA damage-inducible. Despite a strong dependence on LexA, these genes lack LexA boxes and their regulation by LexA is likely to be indirect via unknown factors. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24020

16 Samples

Download data: TSV

(Submitter supplied) Viruses compete with other viruses for limited cellular recourses, and some viruses deliver defense mechanisms that protect the host from competing genetic parasites. PARIS is a defense system, often encoded in viral genomes, that is composed of a 53 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB). Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-EM to determine the structure of this complex which explains how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL21222

6 Samples

Download data: COOL

(Submitter supplied) Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. more...

Organism:

Escherichia coli BW25113

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27123

24 Samples

Download data: CSV, XLSX

(Submitter supplied) Many bacteria are often resistant to antibiotic treatment and drugs because, even if these drugs are effective, bacteria can slow down their growth rate and thus attenuate the effectiveness of the drug. A similar growth-rate control is detected in pathogenic bacteria that infect and persist inside their hosts. The bacterial growth rate within host cells can be regulated by multiple signaling pathways, most of which are still unknown. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23619

4 Samples

Download data: TSV

(Submitter supplied) Many bacteria are often resistant to antibiotic treatment and drugs because, even if these drugs are effective, bacteria can slow down their growth rate and thus attenuate the effectiveness of the drug. A similar growth-rate control is detected in pathogenic bacteria that infect and persist inside their hosts. The bacterial growth rate within host cells can be regulated by multiple signaling pathways, most of which are still unknown. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32269

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Antibiotic treatment typically eliminates a significant portion of a bacterial population, leaving behind a smaller subset of tolerant cells that can survive the treatment. These tolerant cells hinder the effectiveness of the antibiotic, potentially leading to the development of antibiotic resistance within the population. Antibiotic tolerance differs from resistance: tolerant cells are unable to grow or reproduce in the presence of the antibiotic, but they can proliferate once the antibiotic is removed. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

6 Samples

Download data: CSV

(Submitter supplied) Total RNA was extracted and sequenced from Escherichia coli cultured to log phase and stable phase at 37 ° C and 45 ° C, respectively. The transcriptome data of Escherichia coli under four different growth conditions were obtained.

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24659

12 Samples

Download data: TXT

(Submitter supplied) Chromosome conformation capture and sequencing experiments were carried out at 37℃ and 45℃ for E. coli in logarithmic phase and stable phase, respectively. Three-dimensional DNA interaction data of E. coli under four different growth conditions and control group were obtained

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL24659

10 Samples

Download data: TXT

(Submitter supplied) Pathogenic allele silencing is a promising treatment for genetic hereditary diseases. However, the concern about the specificity of present RNA-knockdown strategies has limited their in vivo applications. Here a TaqTth-hpRNA system consisting of a small, chimeric protein (TaqTth) and hairpin-RNA probe (hpRNA) is provided. The TaqTth-hpRNA showed a high-specific knockdown against targeted mRNA with minimal flanking sequence-motif requirement and less cell viability damage, then was applied to mutant APPswe mRNA silencing without altering the wild-type APP mRNA in Alzheimer’s disease. more...

Organism:

Escherichia coli BL21

Type:

Other

Platform:

GPL34578

2 Samples

Download data: TXT

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

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24659

22 Samples

Download data: TXT

(Submitter supplied) The Proline-rich Antimicrobial Peptide (PrAMP) apidaecin (Api) inhibits translation by binding in the ribosomal nascent peptide exit tunnel, trapping release factors RF1 or RF2, and arresting ribosomes at stop codons. To explore the extent of sequence variations of the native 18-amino acid Api that allows it to preserve its activity, we screened a library of synthetic mutant Api genes expressed in bacterial cells, resulting in nearly 350,000 peptide variants with multiple substitutions. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL16085

7 Samples

Download data: TXT, XLSX