GEO DataSets

(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

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(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; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

7 Samples

Download data: CEL, EXP

(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

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) 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) 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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(Submitter supplied) The Escherichia coli quorum-sensing regulator, SdiA, belongs to the LuxR family of transcriptional regulators and is responsible for detecting signals from other bacteria. Previously we found that SdiA is necessary for E. coli to control its biofilm formation with indole just as SdiA is necessary for E. coli to alter its biofilm formation in the presence of N-acylhomoserine lactones (AHLs). Here we engineered SdiA by random mutagenesis to further control biofilm formation in the presence of indole and AHLs. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

3 Samples

Download data: CEL, CHP

(Submitter supplied) Because many virulence genes in E. coli and other pathogens are regulated by temperature, we wanted to determine on a genome-wide scale which genes are modulated in adapting to both human host temperature (37˚C) and ambient room temperature (23˚C). Overall, 126 genes were found to be more highly expressed at 37˚C (1) whereas 297 genes were more highly expressed at 23˚C (2). Genes involved in the uptake and utilization of amino acids, carbohydrates, and iron dominated the 37˚C list, supporting a model in which temperature serves as a host cue to increase expression of bacterial genes needed for growth. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL5942

5 Samples

Download data: GPR, TXT

(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

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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) 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 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) 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) P. aeruginosa PAO1 wild type and PA2663 mutant strains expression in biofilm cells relative to P. aeruginosa PAO1 wild type strain expression in biofilm cells. All samples cultured in LB with glass wool Keywords: Biofilm

Organism:

Pseudomonas aeruginosa

Type:

Expression profiling by array

Platform:

GPL84

2 Samples

Download data: CEL

(Submitter supplied) Quorum signal uptake is an indispensable part of quorum sensing regulations. The coperative regulation of uptake repressor and kinase precisely signale the cells for quorum sensing uptake and terminate the quorum sensing signal production. We use the DNA microarray to detail the E. coli quorum sensing uptake reuglations and related gene regulations. Keywords: specific growth

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

6 Samples

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(Submitter supplied) Transcriptional profiles of Escherichia coli MG1655 in mixed culture with Pseudomonas aeruginosa PAO1 showed a number of E. coli genes to be upregulated including purA-F and other genes associated with purine synthesis. In contrast, genes associated with pyrimidine synthesis were unaffected. Competition experiments in both planktonic and biofilm cultures, using three purine synthesis mutants, purD, purH, and purT showed little difference in E. more...

Organism:

Pseudomonas aeruginosa; Escherichia coli; Pseudomonas aeruginosa PAO1; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platforms:

GPL3154 GPL84

6 Samples

Download data: CEL, CHP

(Submitter supplied) Transcriptional profiles of Escherichia coli MG1655 in mixed culture with Pseudomonas aeruginosa PAO1 showed a number of E. coli genes to be upregulated including purA-F and other genes associated with purine synthesis. In contrast, genes associated with pyrimidine synthesis were unaffected. Competition experiments in both planktonic and biofilm cultures, using three purine synthesis mutants, purD, purH, and purT showed little difference in E. more...

Organism:

Escherichia coli; Pseudomonas aeruginosa; Pseudomonas aeruginosa PAO1

Type:

Expression profiling by array

Platforms:

GPL84 GPL3154

8 Samples

Download data: CEL, CHP

(Submitter supplied) E. coli K-12 wild type strains gene expression in biofilm cells with R1drd19 relative to that in biofilm cells of E. coli K-12 wild type strains without R1drd19. All the samples were cultured in LB or M9C glu on glass wool at different time. Keywords: biofilm

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

10 Samples

Download data: CEL