GEO DataSets

(Submitter supplied) Single-molecule correlated chemical probing (smCCP) is an experimentally concise strategy for characterizing higher-order structural interactions in RNA. smCCP data yield rich, but complex, structural information on base pairing, conformational ensembles, and tertiary interactions. To date, through-space communication specifically measuring RNA tertiary structure has been difficult to isolate from structural communication reflective of other interactions. more...

Organism:

Enterococcus faecalis

Type:

Other

Platform:

GPL24867

15 Samples

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(Submitter supplied) Sortase-assembled pili contribute to virulence in many Gram-positive bacteria. In Enterococcus faecalis, the endocarditis and biofilm-associated pilus (Ebp) is polymerized on the membrane by sortase C (SrtC) and attached to the cell wall by sortase A (SrtA). In the absence of SrtA, polymerized pili remain anchored to the membrane (i.e. off-pathway). Here we show that the high temperature requirement A (HtrA) bifunctional chaperone/protease of E. more...

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18799 GPL24867

33 Samples

Download data: XLSX

(Submitter supplied) Enterococcus faecalis is a commensal bacterium in the gastrointestinal tract (GIT) of humans and other organisms. Outside of the GIT, E. faecalis can cause infections in root canals, wounds, surgical sites, the urinary tract, and on heart valves. Many of these infections can be polymicrobial, and a variety of toxins and nutritional signals influence interactions between E. faecalis and other microbes. more...

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31169

8 Samples

Download data: TXT

(Submitter supplied) The goal was to identify genes regulated by YvcL (EF0768) by assessing changes in the yvcL deletion mutant relative to the isogenic wild-type. Wild-type E. faecalis OG1 and the mutant lacking yvcL were cultured in Mueller-Hinton broth to exponential phase. Total RNA was purified, depleted for rRNA, and subjected to preparation of mRNA libraries.

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28666

8 Samples

Download data: TXT

(Submitter supplied) There had a total number of 804 genes with transcript difference, including 482 up-regulated genes and 322 down-regulated genes. Enrichment analysis of those 804 different transcript gene sets was performed to explore the biological effects and the corresponding pathways that are significantly associated on GO and KEGG (Padj <0.05 as the threshold for significant enrichment). In the GO functional enrichment analysis, all differential genes were significantly enriched into 65 GO Terms, among them there had 50 GO terms belonging to BP (Biological Process). more...

Organism:

Enterococcus durans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30933

12 Samples

Download data: TXT

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

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23172

20 Samples

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(Submitter supplied) Enterococcus faecalis is commonly isolated from different wound types. However, despite its prevalence, the pathogenic mechanisms of E. faecalis during wound infections remain poorly understood. We adopted an in vivo E. faecalis transposon sequencing and RNA sequencing approach to identify fitness determinants that are crucial for replication and persistence of E. faecalis during wound infections in a mouse model. more...

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23172

12 Samples

Download data: TXT

(Submitter supplied) Enterococcus faecalis is commonly isolated from different wound types. However, despite its prevalence, the pathogenic mechanisms of E. faecalis during wound infections remain poorly understood. We adopted an in vivo E. faecalis transposon sequencing and RNA sequencing approach to identify fitness determinants that are crucial for replication and persistence of E. faecalis during wound infections in a mouse model. more...

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23172

8 Samples

Download data: TXT

(Submitter supplied) We report the transcriptome of cultures of WT pMSP3535-PnisA-6his-ftsH(H456Y) and WT pMSP3535-PnisA-6his-ftsH following overnight induction with 125 ng/mL nisin

Organism:

Enterococcus faecalis OG1RF

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32192

6 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to determine how the method of pooling (combining mutants) for bacteral Tn libraries affected mutant distribution. Previously we generated a pooled version of a~6,800 Tn mutant library in Enterococcus faecalis OG1RF by plating and scraping individual mutants. Here, we combined liquid cultures grown in deep well plates. DNA from the new pooled library was extracted, and TnSeq was used to compare mutant distribution between the old (plate scraping) and new (liquid pooling) Tn library formats. more...

Organism:

Enterococcus faecalis

Type:

Other

Platform:

GPL30343

3 Samples

Download data: TXT

(Submitter supplied) To explain the particular behavior of the mutant ΔpnpA strain, we performed a comparative transciptomic analysis of RNA isolated from a derivative strain ΔpnpA mutant versus the wild-type (WT) , after 3h and 6 h of growth in GM17 medium under semi-aerobic conditions.

Organism:

Enterococcus faecalis

Type:

Expression profiling by array

Platform:

GPL28480

12 Samples

Download data: GPR, XLSX

(Submitter supplied) The microbiome has revealed itself as a key player in health and disease. To better understand its role, in addition to microbial diversity, it is important to understand species-specific activity and gene expression. While metatranscriptomics investigates mRNA abundance2, it does not inform about faster post-transcriptional regulation3. Although prokaryotic translation is a common target for antibiotics, a direct measurement of microbiome ribosome dynamics remains inaccessible. more...

Organism:

Escherichia coli; Synechocystis sp. PCC 6803; Staphylococcus aureus; Bacillus amyloliquefaciens; Lactiplantibacillus plantarum; Cryptococcus neoformans; Caulobacter vibrioides; Segatella copri; Alistipes finegoldii; Hoylesella timonensis; compost metagenome; Listeria monocytogenes; Saccharomyces cerevisiae; Salmonella enterica; Parabacteroides merdae; Enterococcus faecalis; Bacillus subtilis; Limosilactobacillus reuteri; Limosilactobacillus fermentum; human feces metagenome

Type:

Other

17 related Platforms

199 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) In this study, we introduce BacDrop, a bacterial droplet-based high throughput scRNA-seq technology that can be applied to large cell numbers. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and elucidated their critical, genome-wide heterogeneity in the absence and presence of antibiotic perturbations.

Organism:

Escherichia coli; Pseudomonas aeruginosa; Klebsiella pneumoniae; Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

5 related Platforms

35 Samples

Download data: TSV, TXT

(Submitter supplied) To identify the genes and pathways utilized by E. faecalis to grow under iron starvation, we used RNA deep sequencing (RNA-seq) to compare the transscriptome of the parent strain OG1RF grown to mid-log in the chemically defined FMC medium with or without the addition of FeSO4 as an iron source.

Organism:

Enterococcus faecalis OG1RF

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32954

6 Samples

Download data: CSV

(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 faecium Aus0004; Enterococcus faecalis V583

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25048 GPL25049

46 Samples

Download data: FASTA, GFF, WIG

(Submitter supplied) To investigate the transcriptional changes that Enterococcus faecalis undergoes during agar surface-penetration, which promote cell envelope remodeling and tolerance to stress.

Organism:

Enterococcus faecalis OG1RF

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32603

18 Samples

Download data: XLSX

(Submitter supplied) Clostridioides difficile is one of the most common nosocomial pathogens and a global public health threat. Upon colonization of the gastrointestinal tract, C. difficile is exposed to a rapidly changing polymicrobial environment and a dynamic metabolic milieu. Despite the link between the gut microbiota and susceptibility to C. difficile, the impact of synergistic interactions between the microbiota and pathogens on the outcome of infection is largely unknown. more...

Organism:

Enterococcus faecalis; Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29669 GPL22510 GPL23172

9 Samples

Download data: BW, TSV

(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) Enterococcus faecalis is often co-isolated with Pseudomonas aeruginosa in mixed-species biofilm-associated infections of wounds and the urinary tract. As a defence strategy, the host innately restricts iron availability at infection sites. Despite their co-prevalence, the polymicrobial interactions of these two pathogens in low iron conditions, such as those found in the host, remains unexplored. Here we show that E. more...

Organism:

Pseudomonas aeruginosa; Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23172 GPL31024 GPL18287

30 Samples

Download data: TXT

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

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31131 GPL23172

45 Samples

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