GEO DataSets

Analysis of enterohemorrhagic Escherichia coli biofilm treated with 7-hydroxyindole or oxidized indole (isatin). Many bacterial oxygenases readily convert indole, an interspecies biofilm signal, into oxidized compounds. Results provide insight into the role of oxidized indoles in biofilm formation.

Organism:

Escherichia coli

Type:

Expression profiling by array, count, 3 agent, 2 cell type sets

Platform:

GPL3154

Series:

GSE6195

4 Samples

Download data: CEL

(Submitter supplied) For the microarray experiments, 10 g glass wool (Corning Glass Works, Corning, N.Y.) were used to form biofilms (30) in 250 mL in 1 L Erlenmeyer shake flasks which were inoculated with overnight cultures diluted that were 1:100. For EHEC with 7-hydroxyindole and isatin, 1000 mM 7-hydroxyindole in 250 mL DMF, 250 mM isatin in 250 mL DMF, or 250 mL DMF alone were added to cells grown in LB. The cells were shaken at 250 rpm and 30°C for 7 hours to form biofilms on the glass wool, and RNA was isolated from the suspension cells and the biofilm. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Dataset:

GDS2753

Platform:

GPL3154

4 Samples

Download data: CEL

(Submitter supplied) Expression in biofilm cells of mutants yceP and yliH relative to biofilm cells of E. coli K-12 wild type strain Keywords: comparison of strain expression profiles

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

4 Samples

Download data

(Submitter supplied) Intercellular signal indole and its derivative hydroxyindoles inhibit Escherichia coli biofilm and diminish Pseudomonas aeruginosa virulence. However, indole and bacterial indole derivatives were unstable in microbial community due to the widespread of diverse oxygenases that could quickly degrade them. Hence, we sought to identify novel non-toxic, stable, and potent indole derivatives from plant sources for inhibiting biofilm formation of E. more...

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

2 Samples

Download data: CEL, CHP

(Submitter supplied) Intercellular signal indole and its derivative hydroxyindoles inhibit Escherichia coli biofilm and diminish Pseudomonas aeruginosa virulence. However, indole and bacterial indole derivatives were unstable in microbial community due to the widespread of diverse oxygenases that could quickly degrade them. Hence, we sought to identify novel non-toxic, stable, and potent indole derivatives from plant sources for inhibiting biofilm formation of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) E. coli K-12 ATCC 25404 in LB medium with 5-fluorouracil 10 uM biofilm cells relative to E. coli K-12 ATCC 25404 in LB DMF biofilm cells. The same amount of stock 5-fluoroacil stock solution (0.1% of the volume) was added as DMF into the LB DMF.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

4 Samples

Download data: CEL

(Submitter supplied) Gene expression of (i) K-12 yceP biofilms upon addition of 600 µM indole in LB glu medium, (ii) K-12 biofilms due to the trpE mutation in LB glu medium, and (iii) K-12 biofilms due to the tnaA mutation in LB medium. Keywords: indole effect and cell type comparison

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL199

7 Samples

Download data: CEL, EXP

(Submitter supplied) E coli O157H7 (EHEC) wildtype 7 hour biofilm cells studied in LB glucose medium with and without chemicals - Epinephrine, Norepinephrine and Indole. Biofilm cells were cultured from glass wool. Keywords: Effect of different chemicals on EHEC gene expression

Organism:

Escherichia coli

Type:

Expression profiling by array

Dataset:

GDS2879

Platform:

GPL3154

4 Samples

Download data: CEL, RPT

Analysis of enterohemmorhagic Escherichia coli (EHEC) O157:H7 treated with epinephrine (EP), norepinephrine (NE), and indole. During infection in the gastrointestinal tract, EHEC is exposed to a wide range of signaling molecules such as EP and NE, and bacterial signaling molecules such as indole.

Organism:

Escherichia coli

Type:

Expression profiling by array, count, 4 agent sets

Platform:

GPL3154

Series:

GSE5552

4 Samples

Download data: CEL, RPT

(Submitter supplied) Contamination with enterohemorrhagic Escherichia coli O157:H7 (EHEC) is a worldwide problem but there is no effective therapy available for EHEC infection. Biofilm formation is closely related with EHEC infection and is one of the mechanisms of antimicrobial resistance. Antibiofilm screening of 560 plant secondary metabolites against EHEC shows that ginkgolic acids C15:1 and C17:1 at 5 μg/ml and Ginko biloba extract at 100 μg/ml significantly inhibited EHEC biofilm formation on the surface of polystyrene, nylon membrane, and glass. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP, XLS

(Submitter supplied) Honey has been widely used against bacterial infection for centuries. Previous studies suggested that honeys in high concentrations inhibited bacterial growth due to the presence of anti-microbial compounds, such as methylglyoxal, hydrogen peroxide, and peptides. In this study, we found that three honeys (acacia, clover, and polyfloral) in a low concentration as below as 0.5% (v/v) significantly suppress virulence and biofilm formation in enterohemorrhagic E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) Pathogenic biofilms have been associated with persistent infections due to their high resistance to antimicrobial agents. To identify non-toxic biofilm inhibitors for enterohemorrhagic Escherichia coli O157:H7, indole-3-acetaldehyde was used and reduced E. coli O157:H7 biofilm formation. Global transcriptome analyses revealed that indole-3-acetaldehyde most repressed two curli operons, csgBAC and csgDEFG, and induced tryptophanase (tnaAB) in E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP, XLSX

(Submitter supplied) Pathogenic biofilms have been associated with persistent infections due to high resistance to antimicrobial agents while commensal biofilms often fortify host immune system. Hence, controlling biofilm formation of both pathogenic bacteria and commensal bacteria is important in bacteria-related diseases. We investigated the effect of plant flavonoids on biofilm formation of both enterohemorrhagic Escherichia coli O157:H7 and three commensal E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) Temporal expression of biofilm and suspenion samples from E. coli wild type cultured on glass wool in LB medium. Samples removed after 4, 7, 15, and 24 hr of culturing Keywords: time course (temporal exression)

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Dataset:

GDS2768

Platform:

GPL199

8 Samples

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Analysis of Escherichia coli K-12 biofilms up to 24 hours of culturing. Biofilm bacteria predominate in nutrient-sufficient ecosystems. Results provide insight into the molecular mechanisms underlying biofilm development.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array, count, 2 cell type, 4 time sets

Platform:

GPL199

Series:

GSE3905

8 Samples

Download data

(Submitter supplied) We have shown the quorum-sensing signals acylhomoserine lactones (AHLs), autoinducer-2 (AI-2), and indole influence the biofilm formation of Escherichia coli. Here, we investigate how the environment, i.e., temperature, affects indole and AI-2 signaling in E. coli. We show in biofilms that indole addition leads to more extensive differential gene expression at 30°C (186 genes) than at 37°C (59 genes), that indole reduces biofilm formation (without affecting growth) more significantly at 25°C and 30°C than at 37°C, and that the effect is associated with the quorum-sensing protein SdiA. more...

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platforms:

GPL199 GPL3154

14 Samples

Download data: CEL, CHP

(Submitter supplied) E. coli K-12 BW25113 mutant strain ycfR expression in biofilm cells relative to E. coli wild-type strain expression in biofilm cells. All samples cultured in LB glu with glass wool Keywords: Cell type comparison

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL199

2 Samples

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(Submitter supplied) E. coli K-12 BW25113 mutant strain yncC expression in biofilm cells relative to E. coli wild-type strain expression in biofilm cells. All samples were cultured in LB with glasswool at 37C for 15 hours and E. coli K-12 MG1655 mutant yncC colony cells vs wild type colony cells in LB plates 15h 37C. Quorum-sensing signal autoinducer 2 (AI-2) stimulates Escherichia coli biofilm formation through the motility regulator MqsR that induces expression of the putative transcription factor encoded by yncC. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platforms:

GPL199 GPL3154

4 Samples

Download data: CEL, CHP

(Submitter supplied) Two lineages of enterohemorrhagic (EHEC) Escherichia coli O157:H7 (EDL933, Stx1+ and Stx2+) and 86-24 (Stx2+) were investigated in regards to biofilm formation on an abiotic surface. Strikingly, EDL933 strain formed a robust biofilm while 86-24 strain formed no biofilm on either a polystyrene plate or a polyethylene tube. To identify the genetic mechanisms of different biofilm formation in two EHEC strains, DNA microarrays were first performed and phenotypic assays were followed. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

2 Samples

Download data: CEL, CHP

(Submitter supplied) The E. coli Genechip antisense genome array was used to study the differential gene expression profile of E. coli K12 ydgG mutant compared to its isogenic wild type in a mature biofilm. Keywords: E. coli K12 antisense chip

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL199

2 Samples

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