GEO DataSets

(Submitter supplied) Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. more...

Organism:

Salmonella enterica; Enterobacter cloacae; Escherichia coli; Klebsiella pneumoniae; Serratia marcescens; Citrobacter rodentium

Type:

Expression profiling by high throughput sequencing

6 related Platforms

64 Samples

Download data: TXT

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

Organism:

Clostridium senegalense; Escherichia coli

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL34292

8 Samples

Download data: BW

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...

Organism:

Clostridium senegalense; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21222 GPL34292

4 Samples

Download data: BW

(Submitter supplied) TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life. IS605-family TnpB homologs function in bacteria as programmable RNA-guided homing endonucleases driving transposon maintenance through DSB-stimulated homologous recombination. Here we uncover molecular mechanisms of transposition lifecycle of IS607-family elements that, remarkably, also encode group I introns. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL21222

4 Samples

Download data: BW

(Submitter supplied) Proteins function in crowded cellular environments in which they must bind to specific target proteins but also avoid binding to many other off-target proteins. In large protein families this task is particularly challenging because many off-target proteins have very similar structures. How this specificity of physical protein-protein interactions in cellular networks is encoded and evolves is not very well understood. more...

Organism:

Escherichia coli; Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL17342 GPL21222

19 Samples

Download data: TXT

(Submitter supplied) Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. more...

Organism:

Enterobacter cloacae; Escherichia coli; Enterobacter sp. BIDMC93

Type:

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

4 related Platforms

51 Samples

Download data: BED, BW, XLSX

(Submitter supplied) In 2011, in Germany, Escherichia coli O104:H4 caused the enterohemorrhagic E. coli (EHEC) outbreak with the highest incidence rate of hemolytic uremic syndrome. This pathogen carries an exceptionally potent combination of EHEC- and enteroaggregative E. coli (EAEC)-specific virulence factors. Here, we identified an E. coli O104:H4 isolate that carried a single nucleotide polymorphism (SNP) in the start codon (ATG>ATA) of rpoS, encoding the alternative sigma factor S. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

12 Samples

Download data: CSV

(Submitter supplied) We assume that adaptation to tisB expression is driven by cellular stress responses. It has already been observed that expression of type I toxins leads to up-regulation of several stress-related genes. To reveal the response to TisB on a global scale, transcriptome analysis of MG1655 p0SD-tisB was performed.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

12 Samples

Download data: XLSX

(Submitter supplied) Genome-wide knockout or knockdown screens have become powerful tools for the investigation of genotype-to-phenotype relationships. In bacteria, these screens commonly rely on transcriptional repression by dCas9, gene knockouts through Cas9 editing or random transposon mutagenesis, but depending on the technique, suffer from incomplete gene silencing, low editing efficiencies or they require massive library sizes. more...

Organism:

Escherichia coli

Type:

Other

Platforms:

GPL21222 GPL25368

27 Samples

Download data: CSV

(Submitter supplied) PRO-seq experiments in multiple organisms. Also, PRO-seq experiment of Nelfb and Nelfe degron mESC in serum/LIF with or without dTAG-13. 

Organism:

Dictyostelium discoideum; Capsaspora owczarzaki; Creolimax fragrantissima; Haloferax mediterranei; Dryas iulia; Nematostella vectensis; Escherichia coli; Mus musculus; Perkinsus marinus; Daphnia pulex; Strongylocentrotus purpuratus; Sphaeroforma arctica

Type:

Other

12 related Platforms

46 Samples

Download data

(Submitter supplied) Bacteria harbor diverse mechanisms to defend themselves against their viral predators, bacteriophages. In response, phages can evolve counter-defense systems, most of which remain poorly understood. In T4-like phages, the gene tifA prevents bacterial defense by the type III toxin-antitoxin (TA) system toxIN, but the mechanism by which TifA inhibits toxIN remains unclear. Here, we show that TifA directly binds both the endoribonuclease ToxN and RNA, leading to the formation of a high molecular weight ribonucleoprotein complex in which ToxN is inhibited. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

8 Samples

Download data: CSV

(Submitter supplied) Plant-associated outbreaks with enterohemorrhagic E. coli (EHEC) increased worldwide during the last decades. Agricultural soil is an important contamination source for edible plants. Thus, the survival of pathogenic E. coli in agricultural soil samples was analyzed in previous studies. Thereby, the influence of environmental factors and biotic factors was investigated. In the current study, genetic factors that influence the survival of enterohemorrhagic/enteroaggregative E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

9 Samples

Download data: TXT

(Submitter supplied) The inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. more...

Organism:

Escherichia coli

Type:

Other

Platforms:

GPL32081 GPL21222 GPL28771

42 Samples

Download data: TXT

(Submitter supplied) The rise of antimicrobial resistant pathogens calls for new antibacterial treatments, but potent new compounds are scarce. Development of new antibiotics is difficult, especially against Gram-negative bacteria, as here uptake is strongly hindered by the additional outer membrane. Most antimicrobial agents against Gram-negatives use the porin mediated pathway to cross the outer membrane, which limits the choice of an antibiotic, as it has to fit by size, charge and hydrophilicity. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

15 Samples

Download data: TXT

(Submitter supplied) mRNA sequencing in bacteria is challenging due to the abundance of ribosomal rRNA that cannot be easily removed prior to sequencing. While commercially available kits target specific rRNA sequences found in defined lists of common bacterial species, they are frequently inefficient when applied to other divergent species, including those from environmental isolates. Similar to the commercial kits, other common techniques for rRNA depletion typically employ large probe sets that tile full-length rRNA sequences; however, such approaches are both time consuming and expensive when applied to multiple species or complex consortia of non-model microbes. more...

Organism:

Caecomyces churrovis; Escherichia coli; Fibrobacter succinogenes; Geobacter metallireducens; Anaeromyces robustus

Type:

Expression profiling by high throughput sequencing

10 related Platforms

65 Samples

Download data: TXT

(Submitter supplied) We performed iterative rounds of massively parallel reporter assay experiments in ex vivo retinas to generate training data for machine learning models of the photoreceptor cis-regulatory grammar.

Organism:

Escherichia coli; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

42 Samples

Download data: COUNTS, FASTA

(Submitter supplied) The alternative sigma factor RpoS regulates transcription of many genes in Escherichia coli in response to many different stresses. The rate of change of RpoS levels in response to stress, and the consequences of that change for the temporal patterns of expression of RpoS-regulated genes has not been described. We measured the temporal pattern of RpoS levels in response to the entry to stationary phase, high osmolarity, or low temperature. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

192 Samples

Download data: TXT

(Submitter supplied) Antimicrobial resistance is a leading mortality factor worldwide. Here we report the discovery of clovibactin, a new antibiotic, isolated from uncultured soil bacteria. Clovibactin efficiently kills drug-resistant Gram-positivebacterial pathogens without detectable resistance. Using biochemical assays,solid-state NMR, and atomic force microscopy, we dissect its mode of action. Clovibactin blocks cell wall synthesis by targeting pyrophosphate of multiple essential peptidoglycan precursors (C55PP, Lipid II, LipidWTA). more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

12 Samples

Download data: TXT

(Submitter supplied) The microbiome is an underappreciated contributor to intestinal drug metabolism with broad implications for drug efficacy and toxicity. While considerable progress has been made towards identifying the gut bacterial genes and enzymes involved, the role of environmental factors in shaping their activity remains poorly understood. Here, we focus on the gut bacterial reduction of azo bonds (R-N=N-R’), found in diverse chemicals in both food and drugs. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

23 Samples

Download data: CSV

(Submitter supplied) We replaced the natural pnp locus with the human cDNA and studied the transcriptomes of 3 strains, namely the wt pnp+ (C-1a), the mutant with pnp ORF deletion (C-5691) and the strain with the substitution of the bacterial ORF with the human one (C-6001), before and 4 minutes after the addition of rifampicin to inhibit transcription.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

24 Samples

Download data: TXT