txid91061[Organism] - GEO DataSets

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Select item 2002787911.

RNA sequencing of Streptococcus salivarius strains from oral cavities of Korean subjects

(Submitter supplied) To investigate the subspecies level differences in the expression profiles of Streptococcus salivarius strains, we conducted the RNA sequencing analysis of Streptococcus salivarius strains.

Organism:: Streptococcus salivarius

Type:: Expression profiling by high throughput sequencing

Platform:: GPL34965
24 Samples

Download data: TXT

Series

Accession:: GSE278791

ID:: 200278791

Select item 2002806922.

RNA-seq Analysis of Enterococcus faecalis in Response to Surfactin Treatment

(Submitter supplied) We found that biofilm formation ability of E. faecalis was impacted by surfactin. To further understand how E. faecalis responded to surfactin, we searched for differentially expressed genes between E. faecalis treated with or without surfactin using RNA-seq analysis.

Organism:: Enterococcus faecalis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL35064
2 Samples

Download data: XLSX

Series

Accession:: GSE280692

ID:: 200280692

Select item 2002709863.

Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure

(Submitter supplied) Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display vast metabolic and transcriptional diversity along with high recalcitrance to antibiotics and host immune defenses. Investigating the complex heterogeneity within biofilm has been hindered by the lack of a sensitive and high-throughput method to assess stochastic transcriptional activity and regulation between bacterial subpopulations, which requires single-cell resolution. more...

Organism:: Staphylococcus aureus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28116
2 Samples

Download data: TXT

Series

Accession:: GSE270986

ID:: 200270986

Select item 2002694734.

Virulence regulates and boosts CRISPR-Cas9 immunity in Group B Streptococcus.

(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:: GPL28679 GPL25368 GPL29157
26 Samples

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Series

Accession:: GSE269473

ID:: 200269473

Select item 2002694725.

Virulence regulates and boosts CRISPR-Cas9 immunity in Group B Streptococcus [RNA-seq]

(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:: Streptococcus agalactiae

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29157
18 Samples

Download data: TXT

Series

Accession:: GSE269472

ID:: 200269472

Select item 2002694716.

Virulence regulates and boosts CRISPR-Cas9 immunity in Group B Streptococcus [CrispRseq]

Organism:: Escherichia coli; Streptococcus agalactiae

Type:: Other

Platforms:: GPL28679 GPL25368
8 Samples

Download data: XLSX

Series

Accession:: GSE269471

ID:: 200269471

Select item 2002804987.

Characterisation of a novel covS SNP identified in Australian Group A Streptococcus isolates derived from the M1UK lineage

(Submitter supplied) Group A Streptococcus (GAS) is a human-adapted pathogen responsible for a variety of diseases. The GAS M1UK lineage has contributed significantly to the recently reported increases in scarlet fever and invasive infections, however the basis for its evolutionary success is not yet fully understood. During the transition to systemic disease, the M1 serotype is known to give rise to spontaneous mutations in the CovRS two-component transcriptional regulation system that confer a fitness advantage during invasive infections. more...

Organism:: Streptococcus pyogenes

Type:: Expression profiling by high throughput sequencing

Platform:: GPL28678
12 Samples

Download data: TSV

Series

Accession:: GSE280498

ID:: 200280498

Select item 2002784228.

Fingerprinting tertiary structure in complex RNAs using single-molecule correlated chemical probing

(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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Series

Accession:: GSE278422

ID:: 200278422

PubMed Similar studies

Select item 2002791879.

TEAL-seq (Targeted Expression Analysis Sequencing) of S. aureus and S. epidermidis in TSB and skin-relevent conditions

(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

Series

Accession:: GSE279187

ID:: 200279187

Select item 20018595810.

Comparative transcriptomics analysis of L-alanine-induced Bacillus subtilis S-2 and 312 strains

(Submitter supplied) Two wide type strains of Bacillus subtilis, S-2 and 312, were selected to study their genic differences treated by L-alanine through comparative transcriptomics analysis. The spores of B. subtilis S-2 were selected because of their high germination potential to L-alanine. The spores of B. subtilis 312 without a response to L-alanine were used as the control. The spores with or without L-alanine (100 mm) pretreatment were both cultured in the synthetic medium for 9 h, and then collected for sequencing.

Organism:: Bacillus subtilis

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29318
8 Samples

Download data: TXT

Series

Accession:: GSE185958

ID:: 200185958

SRA Run Selector

Select item 20025351611.

The transcriptional program of Staphylococcus aureus phage K is affected by a host rpoC mutation that confers phage K resistance

(Submitter supplied) To better understand host/phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 S. aureus clinical isolate NRS384 that were resistant to phage K. Six of these had a single missense mutation in the host rpoC gene, which encodes the RNA polymerase beta prime subunit. To examine the hypothesis that the mutations in the host RNA polymerase affect the transcription of phage genes, we performed RNA-seq analysis on total RNA samples collected from NRS384 wild-type (WT) and rpoC G17D mutant cultures infected with phage K, at different time points after infection. more...

Organism:: Staphylococcus aureus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27158
56 Samples

Download data: XLSX

Series

Accession:: GSE253516

ID:: 200253516

Select item 20026939312.

Listeria monocytogenes transcriptional response to low concentrations of paracetic acid (PAA)

(Submitter supplied) Peracetic acid (PAA), a strong oxidizing agent, has been widely used as a disinfectant in food processing settings as it does not produce harmful chlorinated by-products. In the present study, the transcriptional response of Listeria monocytogenes to 2.5 ppm of PAA was assessed using RNA-sequencing (RNA-seq). Our analysis revealed 12 differentially expressed genes, of which 9 were up-regulated (ohrR, ohrA, rpsN, lmo0637, lmo1973, fur, lmo2492, zurM, and lmo1007), and 3 were down-regulated (argG, lmo0604, lmo2156) in PAA treated samples compared to the control samples. more...

Organism:: Listeria monocytogenes

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27107
18 Samples

Download data: TAB

Series

Accession:: GSE269393

ID:: 200269393

Select item 20026824613.

Untargeted and targeted transcriptome analysis to decipher the impact of exogenous fatty acids in cold stress adaptation of Listeria monocytogenes

(Submitter supplied) Listeria monocytogenes is a ubiquitous and psychrophilic foodborne pathogen commonly found in raw materials, ready to eat products and food environments. It was previously demonstrated that L. monocytogenes can grow faster at low temperature when unsaturated fatty acids (UFA) are present in its environment. In this study, we used comparative gene expression profiling of RNA-sequencing data to understand the impact of UFA on the behavior and cold adaptation of L. more...

Organism:: Listeria monocytogenes

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26477
12 Samples

Download data: TXT

Series

Accession:: GSE268246

ID:: 200268246

PubMed Full text in PMC Similar studies

Select item 20025178314.

Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions

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

Organism:: Serratia marcescens; Lactiplantibacillus plantarum

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL33401 GPL30015 GPL34033
30 Samples

Download data: MTX, TSV, TXT

Series

Accession:: GSE251783

ID:: 200251783

Select item 20025178215.

Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions [scRNA-seq]

(Submitter supplied) A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. more...

Organism:: Serratia marcescens; Lactiplantibacillus plantarum

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL33401 GPL34033 GPL30015
6 Samples

Download data: MTX, TSV

Series

Accession:: GSE251782

ID:: 200251782

Select item 20025178116.

Drosophila and Commensal Bacteria Synergistically Compete with Opportunistic Pathogens at Bulk and Single-Cell Resolutions [bulkRNA-seq]

Organism:: Lactiplantibacillus plantarum; Serratia marcescens

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL34033 GPL30015 GPL33401
24 Samples

Download data: TXT

Series

Accession:: GSE251781

ID:: 200251781

Select item 20026135717.

Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme

(Submitter supplied) Like other functional RNAs, ribozymes contain a conserved catalytic center supported by peripheral domains that vary among ribozyme sub-families. To understand how core-peripheral interactions contribute to ribozyme fitness, we compared the cleavage kinetics of all single base substitutions at 152 sites across the Bacillus subtilis glmS ribozyme by high-throughput sequencing (ClvSeq). The in vitro activity map mirrored phylogenetic sequence conservation in glmS ribozymes, indicating that biological fitness reports all biochemically important positions. more...

Organism:: Bacillus subtilis

Type:: Other

Platform:: GPL29318
12 Samples

Download data: TXT

Series

Accession:: GSE261357

ID:: 200261357

Select item 20024665518.

The five homologous CiaR-controlled sRNAs modulate Streptococcus pneumoniae Zn-resistance

(Submitter supplied) Zn and Mn are essential micronutrients for many bacteria including Streptococcus pneumoniae. While Zn performs vital structural or catalytic roles in certain proteins, in excess, Zn can inhibit Mn uptake by S. pneumoniae and displace, but not functionally replace Mn from key enzymes including superoxide dismutase A (SodA). Here, we show that the Ccn small regulatory RNAs promote S. pneumoniae Mn uptake and resistance to the oxidative stress. more...

Organism:: Streptococcus pneumoniae D39; Streptococcus pneumoniae TIGR4

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL22373 GPL33901
18 Samples

Download data: XLSX

Series

Accession:: GSE246655

ID:: 200246655

Select item 20026097119.

Biodegradable oxygen-evolving metalloantibiotics for spatiotemporal sono-metalloimmunotherapy against orthopaedic biofilm infections

(Submitter supplied) Pathogen-host competition for manganese and intricate immunostimulatory pathways severely attenuates the efficacy of antibacterial immunotherapy against biofilm infections associated with orthopaedic implants. Herein, we introduce an unprecedented spatiotemporal sono-metalloimmunotherapy (SMIT) strategy aimed at efficient biofilm ablation by custom design of ingenious biomimetic metal-organic framework (PCN-224)-coated MnO2-hydrangea nanoparticles (MnPM) as a metalloantibiotic. more...