GEO DataSets

(Submitter supplied) Hypervirulent Klebsiella pneumoniae (hvKp) is a significant pathogen causing severe community-acquired infections, characterized by the presence of a virulence plasmid. The plasmid-encoded regulator of mucoid phenotype A (RmpA) activates the expression of capsule genes, resulting in a hypermucoviscosity phenotype strongly associated with increased virulence. RmpA features a LuxR DNA-binding domain and a signaling-responsive domain, typical of proteins that regulate multiple biological processes. more...

Organism:

Escherichia coli; Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21433 GPL35274

12 Samples

Download data: XLS

(Submitter supplied) Gallium nitrate has been explored as an FDA-approved alternative to treat antibiotic-resistant bacterial strains. Questions remain as it relates to the full-systems response elicited to counteract its toxic effects. We explored the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 hours in the presence of a sublethal concentration of gallium nitrate. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16085

6 Samples

Download data: CSV, TXT

(Submitter supplied) Antimicrobial resistance pose a global thread nowadays. Compounds of natural origin are an important source of drugs used in clinical practice. However, it is important to understand both their principles of efficacy and their molecular mechanism of action. In this study we evaluated antimicrobial potential of t-cinnamaldehyde which is an organic compound found in many plant species, especially in the Cinnamomum genus, such as Cinnamomum zeylanicum and cassia. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

12 Samples

Download data: XLSX

(Submitter supplied) The increasing prevalence of silver nanoparticle (AgNP) resistances in bacteria,such as Escherichia coli(E. coli) has prompted investigations into resistance mechanisms, sparking a debate between flagellin-mediated AgNP precipitation and copper efflux pump (CusCFBA) activation. Our study unveils a sequential progression of AgNP resistance mechanisms, highlighting the regulatory role of envelope stress, including the CpxRA two-component signal transduction system (cpxRA), the phage shock protein systems (Psp), extracytoplasmic function sigma E factor (σE). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18956

9 Samples

Download data: XLS

(Submitter supplied) Escherichia coli is the leading cause of catheter-associated urinary tract infections, caused by biofilm formation on implanted biomaterial surfaces. Understanding the genes that cause cellular adhesion to diverse biomaterial surfaces may aid in the design of targeting anti-biofouling chemicals to prevent these biofilm infections, but our current knowledge on such surfaces is limited. Here, we incorporate a platform of six biomaterials of varying hydrophilicities and stiffnesses and a comprehensive genome-wide CRISPR interference (CRISPRi) library to elucidate genotype-phenotype relationships for cellular adhesion to physicochemically varied biomaterial surfaces in E. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL21222

20 Samples

Download data: CSV

(Submitter supplied) Recent research has indicated the presence of heterochromatin-like regions of extended protein occupancy and transcriptional silencing of bacterial genomes. We utilized an integrative approach to track chromatin structure and transcription in E. coli K-12 across a wide range of nutrient conditions. In the process, we identified multiple loci which act similarly to facultative heterochromatin in eukaryotes, normally silenced but permitting expression of genes under specific conditions. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL21117

64 Samples

Download data: BEDGRAPH

(Submitter supplied) DegP (HtrA: High Temperature Requirement A) is a periplasmic protease with minor chaperone activity that plays a key role in the quality control of protein folding in the envelope of Escherichia coli. Periplasmic and outer membrane proteins that fail to fold in the periplasm can be proteolysed, while others are chaperoned to their native folded state by DegP. In a ΔdegP strain, E. coli is unable to survive the protein folding stress induced at 42º C. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26856 GPL24020

36 Samples

Download data: XLSX

(Submitter supplied) Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin‒antitoxin (TA) systems. However, the physiological functions of TA systems remain obscure. By studying TA families commonly found on colistin-resistant IncI2 mcr-1-bearing plasmids, we discovered that the HicAB TA, acts as a crucial addiction module to increase horizontal plasmid‒plasmid competition.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

3 Samples

Download data: TXT

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

Organism:

Escherichia coli; Shigella flexneri

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL30040 GPL16085

12 Samples

Download data: GFF

(Submitter supplied) The genome-wide analysis was carried out to find out the genes responsible for single and multiple stress in Shigella flexneri 2a str. 2457T. E. coli used as a reference strain. This is RNA-seq data of E.coli K-12 MG1655.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16085

2 Samples

Download data: GFF

(Submitter supplied) Drug-resistant bacteria pose an urgent global health threat, necessitating the development of antibacterial compounds with a novel mode of action. Protein biosynthesis accounts for up to half of the energy expenditure of bacterial cells and consequently inhibiting the efficiency or fidelity of the bacterial ribosome is a major target of existing antibiotics. Here we describe an alternative mode of action to affect the same process; allowing translation to proceed but causing co-translational aggregation of the nascent chain. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16085

10 Samples

Download data: TXT

(Submitter supplied) Microalgae remain an important feedstock for the production of biofuels and bioproducts. Discovery of new species drives innovation for biotransformation, where bioengineering and other technological advances can significantly optimize performance. Production is predicated on deep knowledge of algal behavior predicted from genomic and phenotypic studies. However, prediction and manipulation of behavior, particularly for scale up, remains a challenge. more...

Organism:

Escherichia coli; Microchloropsis salina; Nannochloropsis gaditana

Type:

Methylation profiling by high throughput sequencing

4 related Platforms

25 Samples

Download data: TXT

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

Organism:

Caulobacter vibrioides NA1000; Staphylococcus aureus; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27158 GPL26592 GPL34253

20 Samples

Download data: TXT, XLSX

(Submitter supplied) In contrast to mammalian cells, bacterial cells lack mRNA polyadenylated tails, presenting a hurdle in isolating mRNA amidst the prevalent rRNA during single-cell RNA-seq. This study introduces a novel method, Ribosomal RNA-derived cDNA Depletion (RiboD), seamlessly integrated into the PETRI-seq technique, yielding RiboD-PETRI. This innovative approach offers a cost-effective, equipment-free, and high-throughput solution for bacterial single-cell RNA sequencing (scRNA-seq). more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Staphylococcus aureus; Caulobacter vibrioides NA1000

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34253 GPL27158 GPL26592

19 Samples

Download data: TXT, XLSX

(Submitter supplied) In contrast to mammalian cells, bacterial cells lack mRNA polyadenylated tails, presenting a hurdle in isolating mRNA amidst the prevalent rRNA during single-cell RNA-seq. This study introduces a novel method, Ribosomal RNA-derived cDNA Depletion (RiboD), seamlessly integrated into the PETRI-seq technique, yielding RiboD-PETRI. This innovative approach offers a cost-effective, equipment-free, and high-throughput solution for bacterial single-cell RNA sequencing (scRNA-seq). more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26592

1 Sample

Download data: TXT, XLSX

(Submitter supplied) Adaptation to diverse transcription factor knockouts reveals robustness of transcription regulatory network

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli BW25113

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26592 GPL27123

46 Samples

Download data: CSV

(Submitter supplied) Red fruits are valued for their vitamin C and polyphenol content, but traditional heat preservation methods used in juice and nectar production can significantly reduce these components. Therefore, alternative non-thermal methods are explored to inactivate foodborne pathogens like Escherichia coli while maintaining the nutritional value. However, knowledge about the effects of these technologies on bacterial cells is limited. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34685

21 Samples

Download data: CSV

(Submitter supplied) Biomolecular condensates composed of proteins and RNA are one approach by which cells regulate post-transcriptional gene expression. Their formation typically involves the phase separation of intrinsically disordered proteins with a target mRNA, sequestering the mRNA into a liquid condensate. This sequestration regulates gene expression by modulating translation or facilitating RNA processing. Here, we engineer synthetic condensates using a fusion of an RNA-binding protein, the human Pumilio2 homology domain, and a synthetic intrinsically disordered protein, an elastin-like polypeptide, that can bind and sequester a target mRNA transcript. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33919

12 Samples

Download data: CSV

(Submitter supplied) Disinfectants are essential tools for controlling infectious diseases and maintaining sterile conditions in many medical and food-industry settings. Recent work revealed that a deficiency in the PTS carbohydrate phosphor transfer system confers pan-tolerance to killing by diverse disinfectant types through its interaction with the cAMP-CRP regulatory network. The present work characterized a new pan-tolerance mutant obtained by enrichment using phenol as a lethal probe and an Escherichia coli PTS null mutant as a parental strain. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26856

4 Samples

Download data: TXT

(Submitter supplied) The post-transcriptional process of RNA polyadenylation sits at the crossroads of energy metabolism and RNA metabolism. RNA polyadenylation is catalyzed by poly(A) polymerases which use ATP as a substrate to add adenine residues to the 3’ end of RNAs, which can alter their stability. In E. coli, RNA polyadenylation mediated by the major poly(A) polymerase (PAP I) was previously shown to facilitate degradation of individual RNAs. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21433

24 Samples

Download data: CSV