GEO DataSets

(Submitter supplied) We investigated the RNA-protein interactome of Enterococcus faecalis V583 and Enterococcus faecium Aus0004 by native gradient fractionation of complexes coupled to RNA-sequencing. Whole bacterial cell lysates were analysed by size and density in a glycerol gradient. At native conditions, RNA-protein complexes stay intact and sediment as a whole. Sedimentation profiles of individual RNAs appear correlated in case of interaction in a complex. more...

Organism:

Enterococcus faecalis V583; Enterococcus faecium Aus0004

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25048 GPL25049

46 Samples

Download data: FASTA, GFF, WIG

(Submitter supplied) The enterococci comprise a genus of 49 low-GC content Gram-positive commensal species within the Firmicutes phylum that are known to occupy diverse habitats, notably the gastrointestinal core microbiota of nearly every phylum, including human. Of particular clinical relevance are two rogue species of enterococci, Enterococcus faecalis and the distantly related Enterococcus faecium, standing among the nefarious multi-drug resistant and hospital-acquired pathogens. more...

Organism:

Enterococcus faecium Aus0004; Enterococcus faecalis V583

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25048 GPL25049

12 Samples

Download data: WIG

(Submitter supplied) Grad-seq of Pseudomonas aerugionosa PAO1 at OD 0.3 with and without infection with ΦKZ bacteriophage

Organism:

Phikzvirus phiKZ; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL28760 GPL23999

44 Samples

Download data: TDF

(Submitter supplied) Much of our current knowledge about cellular RNA–protein complexes in bacteria is derived from analyses in gram-negative model organisms, with the discovery of RNA-binding proteins (RBPs) generally lagging behind in Gram-positive species. Here, we have applied Grad-seq analysis of native RNA–protein complexes to a major Gram-positive human pathogen, Clostridioides difficile, whose RNA biology remains largely unexplored. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL25258

40 Samples

Download data: WIG

(Submitter supplied) Regulatory RNAs (sRNAs) are now considered as major players in many physiological and adaptive responses in pathogenic bacteria. sRNAs have been extensively studied in Gram-negative bacteria, but less information is available in Gram-positive pathogens. There is a spread of multidrug-resistant (MDR) opportunistic organisms, grouped as “ESKAPE” pathogens, which comprise enterococci, a leading cause of hospital-acquired infections and outbreaks with emergence of MDR isolates, especially vancomycin-resistant Enterococcus faecium (VREF). more...

Organism:

Enterococcus faecium Aus0004

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23028

4 Samples

Download data: TXT

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

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL23797

28 Samples

Download data: WIG

(Submitter supplied) RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. more...

Organism:

Streptococcus pneumoniae

Type:

Other

Platform:

GPL23797

6 Samples

Download data: WIG

(Submitter supplied) RNA-protein interactions crucially underlie many steps of bacterial gene expression including post-transcriptional control by small regulatory RNAs (sRNAs). In stark contrast with recent progress in Gram-negative bacteria, knowledge about RNA and protein complexes in Gram-positive species remains scarce. Here, we used Grad-seq to draft a landscape of such complexes in Streptococcus pneumoniae, determining the sedimentation profiles of ~88% of the transcripts and ~62% of the proteins of this important human pathogen. more...

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23797

22 Samples

Download data: WIG

(Submitter supplied) Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading organism with respect to global bacterial protein-protein networks. However, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ~85% of all E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

22 Samples

Download data: WIG

(Submitter supplied) The goal was to identify genes that are regulated by cell wall stress (bacitracin treatment) in wild-type cells but not in mutant cells lacking CroR, thereby revealing genes of the CroR regulon. Cells of a mutant lacking CroR or its otherwise isogenic wild-type E. faecalis OG1 were cultured in Mueller-Hinton broth and treated (or not) with bacitracin for 15 min. Total RNA was purified, depleted for rRNA, and subjected to preparation of TruSeq stranded mRNA libraries before sequencing on a NextSeq 550 (76-bp single read run).

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31169

16 Samples

Download data: TXT

(Submitter supplied) New methods for the global identification of RNA-protein interactions have led to greater recognition of the abundance and importance of RNA-binding proteins (RBPs) in bacteria. Here, we expand this tool kit by developing SEC-seq, a method based on a similar concept as the established Grad-seq approach. In Grad-seq, cellular RNA and protein complexes of a bacterium of interest are separated in a glycerol gradient, followed by high-throughput RNA-sequencing and mass spectrometry analyses of individual gradient fractions. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

21 Samples

Download data: WIG

(Submitter supplied) Gene expression plasticity allows bacteria to adapt to diverse environments, tie their metabolism to available nutrients, and cope with stress. This is particularly relevant in a niche as dynamic and hostile as the human intestinal tract, yet transcriptional networks remain largely unknown in gut Bacteroides spp. Here, we map transcriptional units and profile their expression levels in Bacteroides thetaiotaomicron over a suite of 15 defined experimental conditions that are relevant in vivo, such as variation of temperature, pH, and oxygen tension, exposure to antibiotic stress, and growth on simple carbohydrates or on host mucin-derived glycans. more...

Organism:

Bacteroides thetaiotaomicron

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28094

40 Samples

Download data: CSV, XLSX