GEO DataSets

(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:

GPL3154 GPL199

4 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

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(Submitter supplied) The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

4 Samples

Download data: CEL, CHP

(Submitter supplied) The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL199

4 Samples

Download data: CEL, CHP

(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 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) NsrR is a nitric oxide sensitive regulator of transcription. In Escherichia coli, NsrR is a repressor of the hmp gene encoding the flavohemoglobin that detoxifies nitric oxide. Several other transcription units (including ytfE, ygbA and hcp-hcr) are known to be subject to regulation by NsrR. In this study, chromatin immunoprecipitation and microarray analysis was used to identify NsrR binding sites in the chromosome of Escherichia coli strain MG1655. more...

Organism:

Escherichia coli; Escherichia coli str. K-12 substr. MG1655

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6754

3 Samples

Download data: TXT

(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) This Series involves two studies: 1) The gene expression of E. coli K-12 BW25113 ompA mutant strain vs. wild type strain glasswool biofilm cells and E. coli K-12 BW25113 ompA mutant vs. wild type polystyrene biofilm cells. 2) The gene expression of E. coli BW25113 ompA/pCA24N_ompA vs. ompA/pCA24N suspension cells.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platforms:

GPL3154 GPL199

8 Samples

Download data: CEL, CHP

(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) 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) Here evidence is presented that MqsR and B3021 are a novel toxin-antitoxin (TA) system related to biofilm development and quorum sensing. Using whole-transcriptome studies and nickel enrichment DNA binding microarrays coupled with cell survival studies in which MqsR was overexpressed in isogenic mutants, we identified seven genes involved in MqsR toxicity (clpX, clpP, yfjZ, cspD, relB, relE, and hokA). more...

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platforms:

GPL3154 GPL199

10 Samples

Download data: CEL, CHP

(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) 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) Gene expression changes between outside and inside of biofilms were investigated. The gene expression was compared between the outside and inside of the biofilms. At the same time, the gene expressions were also compared with exponential phase and stationary phase in planktonic cells. The gene expression analysis showed that the physiological activities were higher at the outside of the biofilms than those at the inside of the biofilms. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL, DCP

(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) We used arrays to examine the overall transcriptional differences between WT K-12 E. coli, and EHEC 86-24 and their corresponding QseD (yjiE) mutants.

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL, CHP

(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