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Items: 1 to 20 of 501

1.

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

2.

Phage SEP1 hijacks S. epidermidis stationary cells metabolism to replicate

(Submitter supplied) In nature, bacteria often survive in a stationary state, with low metabolic activity. Phages use the metabolic machinery of the host cell to replicate and, therefore, their efficacy against non-dividing cells is usually limited. Nevertheless, it was previously shown that the Staphylococcus epidermidis phage SEP1 has the remarkable capacity to actively replicate in stationary-phase cells, reducing their numbers. more...
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL30249
24 Samples
Download data: XLSX
Series
Accession:
GSE254200
ID:
200254200

PubMed Full text in PMC Similar studies

3.

Genome-wide Transcription Response of Staphylococcus epidermidis to Heat Shock and Medically-Relevant Glucose Levels

(Submitter supplied) Skin serves as both barrier and interface between body and environment. Skin microbes are intermediaries evolved to respond, transduce, or act in response to changing environmental or physiological conditions. Here, we quantify genome-wide changes in gene expression levels for one abundant skin commensal, Staphylococcus epidermidis, in response to an internal physiological signal, glucose levels, and an external environmental signal, temperature. more...
Organism:
Staphylococcus epidermidis ATCC 12228
Type:
Expression profiling by high throughput sequencing
Platform:
GPL34301
28 Samples
Download data: TXT
Series
Accession:
GSE261664
ID:
200261664

PubMed Full text in PMC Similar studies

4.

Characterization of Staphylococcus epidermidis clinical and commensal isolates transcriptome upon interaction with human blood

(Submitter supplied) The release of cells from S. epidermidis biofilms formed on medical devices has been associated with the onset of bloodstream infections, resulting in increased morbidity and mortality rates. This has to do, in part, with the difficulty to accurately diagnose S. epidermidis bloodstream infections. S. epidermidis is a ubiquitous commensal of human skin and mucosa and, thus, a positive blood culture does not always represent an infection, possibly being the result of contamination during blood collection. more...
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17893
6 Samples
Download data: TXT
Series
Accession:
GSE179407
ID:
200179407

PubMed Full text in PMC Similar studies SRA Run Selector

5.

RNA Atlas of Bacterial Human Pathogens Uncovers Stress Dynamics Linked to Bacterial Infections

(Submitter supplied) Pathogenic bacteria encounter a variety of stressful host environments during infection. Their responses to meet these challenges protect them from deadly damages and aid in adaption to harmful environments. Bacterial products critical for this protection are therefore interesting as suitable targets for new antimicrobials. To shed light on the complex array of molecular pathways involved in bacterial stress responses we challenged 32 diverse human pathogenic bacteria to 11 infection related stress conditions and catalogued their transcriptomes. more...
Organism:
Borreliella burgdorferi; Pseudomonas aeruginosa; Legionella pneumophila; Klebsiella pneumoniae; Yersinia pseudotuberculosis; Vibrio cholerae; Streptococcus suis; Streptococcus agalactiae; Streptococcus pneumoniae; Mycobacterium tuberculosis; Burkholderia pseudomallei; Helicobacter pylori; Enterococcus faecalis; Campylobacter jejuni; Francisella tularensis; Acinetobacter baumannii; Neisseria gonorrhoeae; Escherichia coli; Shigella flexneri; Aggregatibacter actinomycetemcomitans; Haemophilus influenzae; Staphylococcus aureus subsp. aureus MRSA252; Staphylococcus aureus subsp. aureus MSSA476; Neisseria meningitidis; Staphylococcus epidermidis; Streptococcus pyogenes; Listeria monocytogenes; Salmonella enterica; Achromobacter xylosoxidans
Type:
Expression profiling by high throughput sequencing
30 related Platforms
1122 Samples
Download data: TXT
Series
Accession:
GSE152295
ID:
200152295

PubMed Full text in PMC Similar studies SRA Run Selector

6.

Comparative transcriptional analysis of Staphylococcus epidermidis biofilm matrix variants in human platelet concentrates  

(Submitter supplied) This study is focused on understanding the molecular basis of protein- and polysaccharide intercellular adhesin (PIA)- mediated biofilm formation by S. epidermidis in PCs. Comparative transcriptomic analysis of S. epidermidis PIA- biofilm positive (AZ22, AZ39) and PIA+ biofilm positive (ST02) strains was performed using a RNAseq approach. Pathway enrichment analysis revealed cellular component GO term (AZ22), two KEGG pathways (AZ39), and two molecular function GO term and 8 KEGG pathways (ST02) were enriched. more...
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23256
16 Samples
Download data: TXT
Series
Accession:
GSE154352
ID:
200154352

SRA Run Selector

7.

RNA sequencing of S. simiae CCM 7213T, S. capitis SK14 and S. epidermidis RP62A strains

(Submitter supplied) The goal of our study was to perform RNA sequencing of whole transcripts to determine and compare the real length of 3’UTRs among closely-related staphylococcal species. We found that most of the mRNAs encoding orthologous genes in staphylococcal species have 3’UTRs with different lengths in addition to sequence variation.
Organism:
Staphylococcus capitis; Staphylococcus epidermidis; Staphylococcus simiae
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL27999 GPL23256 GPL28000
3 Samples
Download data: BW
Series
Accession:
GSE143600
ID:
200143600

PubMed Full text in PMC Similar studies SRA Run Selector

8.

Differential RNA-Seq (dRNA-seq) of Staphylococcus epidermidis PS2 and PS10 isolates

(Submitter supplied) We performed differential RNA-seq of two Staphylococcus epidermidis clinical isolates (PS2 and PS10) to compare their transcription profiles. The isolates were originally obtained from blood cultures during a systemic infection in an immunocompromised patient (Weisser et al. 2010. J Clin Microbiol 48: 2407-2412). They are of clonal origin, but differ phenotypically with respect to extracellular biofilm matrix production. more...
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26150
4 Samples
Download data: WIG
Series
Accession:
GSE126097
ID:
200126097

PubMed Full text in PMC Similar studies SRA Run Selector

9.

Method for absolute quantification of microbial communities by using both microarrays and competitive PCR

(Submitter supplied) We investigated an improved method that combines competitive PCR and microarray techniques. This approach allowed us to quantify specific bacterial groups mounted on DNA chips with accuracy close to that of real-time PCR, despite a measurement at the end point of PCR, and also to estimate the bacterial DNA content in sample DNA.
Organism:
Bacteria; Acinetobacter baumannii; Escherichia coli; Staphylococcus aureus; Staphylococcus epidermidis; Bacillus cereus; Schaalia odontolytica; Fusobacterium nucleatum subsp. nucleatum; Treponema denticola; Cereibacter sphaeroides; Streptococcus gordonii; Streptococcus agalactiae; Enterococcus faecalis; Bifidobacterium adolescentis; Homo sapiens; Prevotella intermedia; Prevotella nigrescens; Campylobacter rectus; Helicobacter pylori; Pseudomonas aeruginosa; Aggregatibacter actinomycetemcomitans; Phocaeicola vulgatus; Capnocytophaga gingivalis; Deinococcus radiodurans; Streptococcus mutans; Streptococcus intermedius; Cutibacterium acnes; Neisseria meningitidis; Porphyromonas gingivalis; Fusobacterium nucleatum; Clostridium beijerinckii; Lactobacillus gasseri; Tannerella forsythia
Type:
Other
Platform:
GPL25612
178 Samples
Download data: CSV
Series
Accession:
GSE125085
ID:
200125085

PubMed Similar studies Analyze with GEO2R

10.

Bioactive compound from marine sponge-derived Streptomyces sp. SBT348 inhibits staphylococcal growth and biofilm formation

(Submitter supplied) Staphylococcus epidermidis, the common inhabitant of human skin and mucosal surfaces has emerged as an important pathogen in patients receiving surgical implants and medical devices. Entering the body via surgical sites and colonizing the medical devices through formation of multi-layered biofilms it leads to refractory and persistent device-related infections (DRIs). Staphylococcal proportions within biofilms are more tolerant to antibiotics and immune responses, and thus are hard-to-treat. more...
Organism:
Staphylococcus epidermidis RP62A
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24569
12 Samples
Download data: TXT, WIG
Series
Accession:
GSE109983
ID:
200109983

11.

Antibacterial mode of action of alpha-mangostin on Staphylococcus epidermidis

(Submitter supplied) Alpha-mangostin (α-MG) is a natural xanthone reported to exhibit rapid bactericidal activity against Gram-positive bacteria, and may therefore have potential clinical application in healthcare sectors. This study sought to identify the antibacterial mode of action of α-MG against Staphylococcus epidermidis RP62A through RNA-sequencing technology.
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24903
1 Sample
Download data: TXT
Series
Accession:
GSE113302
ID:
200113302

PubMed Full text in PMC Similar studies SRA Run Selector

12.

Transcriptome Comparison of phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (10 h)

(Submitter supplied) Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in stationary phase (10 h). Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in stationary phase (10 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. more...
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23256
9 Samples
Download data: XLSX
Series
Accession:
GSE97656
ID:
200097656

PubMed Full text in PMC Similar studies SRA Run Selector

13.

Transcriptome Comparison of phoU Homologies Genes Deletion strain and the Parent Strain in log-phase (6 h).

(Submitter supplied) Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in log-phase (6 h) Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in log-phase (6 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. more...
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23256
9 Samples
Download data: GFF, XLS
Series
Accession:
GSE97400
ID:
200097400

PubMed Full text in PMC Similar studies SRA Run Selector

14.

Characterization of Staphylococcus epidermidis biofilm-released cells (BRC) transcriptome upon interaction with whole human blood and its cellular and soluble components

(Submitter supplied) The release of cells from S. epidermidis biofilms formed on medical devices has been associated with the onset of bloodstream infections resulting in increased morbidity and mortality among infected patients. In order to better understand the role of BRC in the pathogenesis of S. epidermidis biofilm-related infections, the transcriptome of these cells was evaluated upon exposure to human blood components. more...
Organism:
Staphylococcus epidermidis
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17893
6 Samples
Download data: TXT
Series
Accession:
GSE79948
ID:
200079948

PubMed Full text in PMC Similar studies SRA Run Selector

15.

Toxin mediates sepsis caused by methicillin-resistant Staphylococcus epidermidis

(Submitter supplied) Bacterial sepsis is a major killer in hospitalized patients. Coagulase-negative staphylococci (CNS) with the leading species Staphylococcus epidermidis are the most frequent causes of nosocomial sepsis, with most infectious isolates being methicillin resistant. However, which bacterial factors underlie the pathogenesis of CNS sepsis is unknown. While it has been commonly believed that invariant structures on the surface of CNS trigger sepsis by causing an over-reaction of the immune system, we show here that sepsis caused my methicillin-resistant S. more...
Organism:
Staphylococcus epidermidis; Staphylococcus aureus subsp. aureus MW2; Granulibacter bethesdensis; Chlamydia pneumoniae AR39; Borreliella burgdorferi B31; Coxiella burnetii RSA 493; Chlamydia caviae GPIC; Staphylococcus haemolyticus JCSC1435; Staphylococcus epidermidis ATCC 12228; Chlamydia trachomatis D/UW-3/CX; Coxiella burnetii; Rickettsia rickettsii; Chlamydia muridarum; Staphylococcus epidermidis RP62A
Type:
Expression profiling by array
Platform:
GPL4692
15 Samples
Download data: CEL, CHP
Series
Accession:
GSE85265
ID:
200085265

Analyze with GEO2R

16.

Mechanism of gene regulation by a Staphylococcus aureus toxin

(Submitter supplied) Virulence of many bacterial pathogens, including the important human pathogen Staphylococcus aureus, depends on the secretion of frequently high amounts of toxins. Toxin production involves the need for the bacteria to make physiological adjustments for energy conservation. While toxins are primarily known to be targets of gene regulation, such changes may be accomplished by regulatory functions of the toxins themselves. more...
Organism:
Chlamydia pneumoniae AR39; Coxiella burnetii RSA 493; Granulibacter bethesdensis; Staphylococcus epidermidis ATCC 12228; Staphylococcus aureus subsp. aureus MW2; Coxiella burnetii; Rickettsia rickettsii; Staphylococcus aureus; Chlamydia muridarum; Staphylococcus epidermidis RP62A; Chlamydia caviae GPIC; Borreliella burgdorferi B31; Chlamydia trachomatis D/UW-3/CX; Staphylococcus haemolyticus JCSC1435
Type:
Expression profiling by array
Platform:
GPL4692
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE72878
ID:
200072878

PubMed Full text in PMC Similar studies Analyze with GEO2R

17.

TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens.

(Submitter supplied) Background Bacteria rely on efficient gene regulatory mechanisms to switch between genetic programs when they are facing new environments. Although this regulation can occur at many different levels, one of the key steps is the initiation of transcription. Identification of the first nucleotide transcribed by the RNA polymerase is therefore essential to understand the underlying regulatory processes, since this provides insight on promoter strength and binding sites for transcriptional regulators, and additionally reveals the exact 5' untranslated region of the transcripts, which often contains elements that regulate translation. more...
Organism:
Staphylococcus epidermidis; Acinetobacter baumannii; Staphylococcus aureus; Klebsiella aerogenes
Type:
Expression profiling by high throughput sequencing; Other
4 related Platforms
30 Samples
Download data: TSV
Series
Accession:
GSE85110
ID:
200085110

PubMed Full text in PMC Similar studies SRA Run Selector

18.

The mutual effect of Staphylococcus epidermidis and Staphylococcus aureus in dual species biofilms as revealed by RNA-Seq

(Submitter supplied) We examined the differential gene expression of Staphylococcus epidermidis and Staphylococcus epidermidis in dual species biofilms. Therefore, we performed RNA-Seq on single and dual species biofilms and we compared the gene expression levels in dual species biofilms to those in single species biofilms.
Organism:
Staphylococcus epidermidis; Staphylococcus aureus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21653 GPL17452 GPL21652
9 Samples
Download data: XLSX
Series
Accession:
GSE79575
ID:
200079575

PubMed Full text in PMC Similar studies SRA Run Selector

19.

Transcriptomic Analysis of Staphylococcal sRNAs: Insights into Species Specific Adaption and the Evolution of Pathogenesis

(Submitter supplied) Next-generation sequencing technologies have dramatically increased the rate at which new genomes are sequenced. Accordingly, automated-annotation programs have become adept at identifying and annotating protein coding regions, as well as common and conserved RNAs. Additionally, RNAseq techniques have advanced our ability to identify and annotate regulatory RNAs (sRNAs), which remain significantly understudied. more...
Organism:
Staphylococcus epidermidis; Staphylococcus carnosus; Staphylococcus aureus
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL21408 GPL19476 GPL21407
3 Samples
Download data: XLSX
Series
Accession:
GSE77567
ID:
200077567

PubMed Full text in PMC Similar studies SRA Run Selector

20.

Transcriptional profiling of Coxiella burnetii reveals extensive cell wall remodeling in the small cell variant developmental form

(Submitter supplied) A hallmark of Coxiella burnetii, the bacterial cause of human Q fever, is a biphasic developmental cycle that generates biologically, ultrastructurally, and compositionally distinct large cell variant (LCV) and small cell variant (SCV) forms. LCVs are replicating, exponential phase forms while SCVs are non-replicating, stationary phase forms. The SCV has several properties, such as a condensed nucleoid and an unusual cell envelope, suspected of conferring enhanced environmental stability. more...
Organism:
Rickettsia rickettsii; Chlamydia muridarum; Staphylococcus epidermidis RP62A; Chlamydia caviae GPIC; Staphylococcus haemolyticus JCSC1435; Staphylococcus epidermidis ATCC 12228; Staphylococcus aureus subsp. aureus MW2; Granulibacter bethesdensis; Chlamydia pneumoniae AR39; Borreliella burgdorferi B31; Coxiella burnetii RSA 493; Coxiella burnetii; Chlamydia trachomatis D/UW-3/CX
Type:
Expression profiling by array
Platform:
GPL4692
20 Samples
Download data: CEL, CHP
Series
Accession:
GSE74489
ID:
200074489

Analyze with GEO2R

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