GEO DataSets

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

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL25368 GPL28679 GPL29157

26 Samples

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(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other

Platforms:

GPL28679 GPL25368

8 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) 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:

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

Type:

Expression profiling by high throughput sequencing

6 related Platforms

129 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) L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

48 Samples

Download data: TXT

(Submitter supplied) RNA mutations are known to change mobility in native gels. What is not known is if mobility can serve as an effective tool to separate structurally similar (structural homologs) from structurally destabilized variants in a deep-mutation library of an RNA. Here we defined the proportion of a mutant in the native band from native polyacrylamide gel electrophoresis (PAGE) as a native-mobility-fitness score. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL25368

16 Samples

Download data: TXT

(Submitter supplied) Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

11 Samples

Download data: TXT, XLSX

(Submitter supplied) Translational research on the Cre/loxP recombination system focuses on enhancing its specificity by modifying Cre/DNA interactions. Despite extensive efforts, the exact mechanisms governing how Cre distinguishes between substrates remains elusive. Cre recognizes 13 bp inverted repeats, initiating recombination in the 8 bp spacer region. While literature suggests that efficient recombination proceeds between lox sites with non-loxP spacer sequences when both lox sites have matching spacers, experimental validation for this assumption is lacking. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL25368

24 Samples

Download data: TSV

(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; Escherichia coli; Klebsiella variicola

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 GPL28669 GPL34185

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; Homo sapiens; Escherichia coli; Arabidopsis thaliana; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

9 related Platforms

114 Samples

Download data: CSV, TXT

(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) Current methods for R-loop mapping need to perform DNA:RNA immunoprecipitation for each sample individually, with consequent limitations in throughput. Here, we develop and validate mDRIP-seq, a multi-sample barcoding and pooling method for R-loop mapping. We show mDRIP-seq performs equivalently as conventional methods, but with the merits of high throughput and cost-efficiency. We also show the simplicity of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Escherichia coli; Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL24676 GPL24247 GPL25368

6 Samples

Download data: BW

(Submitter supplied) Current methods for R-loop profiling need to perform experiments for each sample individually, with consequent limitations in throughput. Here, based on the barcoding strategy, we develop mDRIP-seq, a high-throughput method showing equivalent performance as conventional methods, but with merits of 7-fold less cost and 6-fold less hand-on time per sample. We also show the simplicity and effectiveness of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Escherichia coli; Arabidopsis thaliana; Mus musculus; Oryza sativa; Saccharomyces cerevisiae; Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

6 related Platforms

384 Samples

Download data: BW, TXT

(Submitter supplied) Current methods for R-loop mapping need to perform DNA:RNA immunoprecipitation for each sample individually, with consequent limitations in throughput. Here, we develop and validate mDRIP-seq, a multi-sample barcoding and pooling method for R-loop mapping. We show mDRIP-seq performs equivalently as conventional methods, but with the merits of high throughput and cost-efficiency. We also show the simplicity of mDRIP-seq for relative and absolute quantitation of genomic R-loop fractions for multiple samples. more...

Organism:

Escherichia coli; Saccharomyces cerevisiae; Arabidopsis thaliana; Oryza sativa; Homo sapiens; Mus musculus

Type:

Other

6 related Platforms

356 Samples

Download data: BW

(Submitter supplied) The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.

Organism:

Escherichia coli; synthetic construct; Arabidopsis thaliana; Danio rerio

Type:

Other; Expression profiling by high throughput sequencing

4 related Platforms

60 Samples

Download data: BW

(Submitter supplied) The dataset contains small RNAs that associated with HrAgo1 during heterologous expression in E. coli. The goal of the study was to determine what type of small RNAs associate with HrAgo1 and from what RNA transcripts these small RNAs are derived

Organism:

Escherichia coli

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25368

1 Sample

Download data: XLSX