GEO DataSets

(Submitter supplied) Whether the emergence of a nascent protein from the ribosome and the formation of structural elements are synchronized has been a longstanding question. Paradoxically, kinetically efficient translation can induce mis-folding and aggregation despite the presence of molecular chaperones, which in Escherichia coli are induced by unfolded protein via σ32. The molecular mechanisms mediating translation efficiency and protein folding efficiency remain poorly understood. more...

Organism:

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

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL18956 GPL18133

30 Samples

Download data: TSV

(Submitter supplied) Salmonella enterica serovar Typhimurium (S. Typhimurium) infection triggers an inflammatory response that changes the concentration of luminal metabolites in the gut, resulting in a distinct environment from a healthy one. We recently demonstrated that S. Typhimurium possesses the ability to form biofilms within the host environment and responds to nitrate as a signaling molecule, enabling it to modulate the transition between sessile and planktonic states. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33626

6 Samples

Download data: XLSX

(Submitter supplied) The effectiveness of antibacterial agents is strongly influenced by its antibacterial mechanism, which, in turn, is dependent on the agent’s topological structure. In addition to oxidative stress (especially caused by reactive oxygen species), known to be a key mechanism for 2D phosphorene structures, physical penetration of bacterial cell membranes is predicted for violet phosphorene nanosheets. In this study, we demonstrate that violet phosphorus (VP) and its exfoliated product, violet phosphorene nanosheets (VPNS), have superior antibacterial capability against pathogens.A series of antibacterial tests and theoretical calculations show that VPNS can inactivate >99.9% of two common pathogens (Escherichia coli and Staphylococcus aureus) and >99% of two “superbugs” (i.e., antibiotic-resistant bacteria, Escherichia coli pUC19 and methicillin-resistant Staphylococcus aureus) via oxidative stress combined with cell membrane penetration by VPNS Moreover, VPNS have higher antibacterial activity than black phosphorene nanosheets in vitro and in vivo. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

6 Samples

Download data: TXT

(Submitter supplied) We present genome-wide RpoD-family sigma factors (RpoD, RpoS, and RpoH) binding profiles and transcriptome profiles in Salmonella Typhimurium 14028s under both control (37°C) and sublethal heat shock conditions (42°C). These genome-scale experimental data show how three RpoD-family sigma factors simultaneously coordinate many types of cellular processes to orchestrate the overall response of S. Typhimurium to heat stress.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28222

12 Samples

Download data: XLSX

(Submitter supplied) We present genome-wide RpoD-family sigma factors (RpoD, RpoS, and RpoH) binding profiles and transcriptome profiles in Salmonella Typhimurium 14028s under both control (37°C) and sublethal heat shock conditions (42°C). These genome-scale experimental data show how three RpoD-family sigma factors simultaneously coordinate many types of cellular processes to orchestrate the overall response of S. Typhimurium to heat stress.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28222

8 Samples

Download data: TSV

(Submitter supplied) Metagenome sequencing enables discovery and genetic characterization of complex microbial communities from diverse ecosystems. However, determining the activity of isolates within a community using transcriptomics presents several challenges including the wide dynamic range of organismal and gene expression abundances, the presence of host RNA, and low microbial biomass at many body sites. To address these limitations, we developed “Targeted Expression Analysis Sequencing” or TEAL-seq. more...

Organism:

Staphylococcus epidermidis; Homo sapiens; Escherichia coli; Staphylococcus aureus; Mus musculus

Type:

Expression profiling by high throughput sequencing

6 related Platforms

129 Samples

Download data: XLSX

(Submitter supplied) Here we present high-resolution Cappable-Seq transcriptomic data on Salmonella gene expression under optimal, starvation and hydrogen peroxide conditions, and after 8 and 15 hours of co-culture with A. Castellanii.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34612

20 Samples

Download data: CSV, TXT

(Submitter supplied) Here we present high-resolution transcriptomic data on Salmonella gene expression under optimal, starvation and hydrogen peroxide conditions, and after 8 and 15 hours of co-culture with A. Castellanii.

Organism:

Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34632

22 Samples

Download data: CSV, TXT

(Submitter supplied) Although many clinically important antibiotics inhibit bacterial ribosomes, the mechanisms by which bacterial cells rescue ribosomes stalled by antibiotics remain poorly understood. Ribosome stalling leads to collisions that recruit ribosome quality control (RQC) factors that recycle the ribosome subunits and target nascent proteins for degradation. Surprisingly, loss of known RQC factors in E. coli does not lead to significant antibiotic sensitivity, even though antibiotics stall ribosomes and induce collisions, suggesting the existence of additional, uncharacterized RQC mechanisms. more...

Organism:

Escherichia coli str. K-12 substr. MG1655

Type:

Other

Platform:

GPL21117

6 Samples

Download data: WIG

(Submitter supplied) Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. more...

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21222

4 Samples

Download data: XLSX

(Submitter supplied) Retrons are bacterial genetic retroelements that encode reverse transcriptase capable of producing multicopy single-stranded DNA (msDNA) and function as antiphage defense systems. Phages employ several strategies to counter the host defense systems, but no mechanisms for evading retrons are known. Here, we show that tRNATyr and Rad (retron anti defense) of T5 phage family inhibit the defense activity of retron 78 and a broad range of retrons, respectively. more...

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL21222

4 Samples

Download data: XLSX

(Submitter supplied) RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli. Here, employing high-throughput RNA sequencing, we explored the impact of Musashi expression on the transcriptomic and translatomic profiles of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

4 Samples

Download data: CSV, TXT

(Submitter supplied) RNA recognition motifs (RRMs) are widespread RNA-binding protein domains in eukaryotes, which represent promising synthetic biology tools due to their compact structure and efficient activity. Yet, their use in prokaryotes is limited and their functionality poorly characterized. Recently, we repurposed a mammalian Musashi protein containing two RRMs as a translation regulator in Escherichia coli. Here, employing high-throughput RNA sequencing, we explored the impact of Musashi expression on the transcriptomic and translatomic profiles of E. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL25368

4 Samples

Download data: CSV, TXT

(Submitter supplied) We performed RNA-Seq to accurately assess the impact of AcK addition or biosynthesis on gene expression in E. coli cells.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

9 Samples

Download data: TXT

(Submitter supplied) Different genetic engineering strategies have been proposed to obtain E. coli strains that selectively consume xylose. In this study, a previously reported strategy for obtaining a xylose-selective strain in E. coli K12 was applied to E. coli BL21 (DE3). While this approach resulted in the expected xylose-selective phenotype, a low xylose consumption rate was recorded when the strain was grown on a mixture of xylose and glucose. more...

Organism:

Escherichia coli BL21(DE3)

Type:

Expression profiling by array

Platform:

GPL34929

2 Samples

Download data: CSV, DOCX, TXT

(Submitter supplied) Antibiotic use can lead to expansion of multi-drug resistant pathobionts within the gut microbiome that can cause life-threatening infections. Selective alternatives to conventional antibiotics are in dire need. Here, we describe a Klebsiella PhageBank that enables the rapid design of antimicrobial bacteriophage cocktails to treat multi-drug resistant Klebsiella pneumoniae. Using a transposon library in carbapenem-resistant K. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34705

4 Samples

Download data: CSV

(Submitter supplied) LF82, an adherent invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn’s disease, an inflammatory bowel disease of unknown etiology. No genetic features have been identified that distinguish AIEC strains, such as LF82, from “commensal” or pathogenic E. coli. We investigated an extremely rare single nucleotide polymorphism (SNP) within the highly conserved rpoD gene, encoding sigma70 [primary sigma factor, RNA polymerase (RNAP)]. more...

Organism:

Escherichia coli LF82

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34117

6 Samples

Download data: CSV, TXT

(Submitter supplied) RNA molecules can populate an ensemble of alternative structural conformations, but the true extent of the RNA secondary structure folding space of a living cell has never been explored. We here generated the first transcriptome-wide maps of RNA secondary structure ensembles in Escherichia coli, both at physiological temperature and upon cold-shock. Our analysis revealed hundreds of novel putative conserved RNA switches.

Organism:

Escherichia coli

Type:

Other

Platforms:

GPL33918 GPL33919

10 Samples

Download data: WIG

(Submitter supplied) Since the molecular mechanisms behind adaptation and the bacterial stress response toward antimicrobial photodynamic therapy (aPDT) are not entirely clear yet, the aim of the present study was to investigate the transcriptomic stress response in Escherichia coli after sublethal treatment with aPDT using RNA sequencing (RNA-Seq). Planktonic cultures of stationary phase E. coli were treated with aPDT using a sublethal dose of the photosensitizer SAPYR. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

20 Samples

Download data: TSV

(Submitter supplied) The non-typhoidal Salmonella enterica serotype Heidelberg is a major foodborne pathogen primarily transmitted to humans through contaminated poultry products. Current control measures emphasize novel approaches to mitigate Salmonella Heidelberg colonization in poultry and the contamination of poultry products, thereby reducing its transmission to humans. This study highlight that commensal E. coli 47-1826 can potentially be used to control of S. more...

Organism:

Escherichia coli; Salmonella enterica subsp. enterica serovar Heidelberg

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34889 GPL34890 GPL16085

9 Samples

Download data: TXT