GEO DataSets

(Submitter supplied) Glyphosate (GLY) is an effective antimetabolite that acts against the shikimate pathway 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, However, little is known about the genome-scale transcriptional responses of bacteria after glyphosate shock. To investigate further the mechanisms by which E. coli response to a glyphosate shock, a DNA-based microarray was used for transcriptional analysis of E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL

(Submitter supplied) Triclosan is a biocidal active agent commonly found in domestic cleaning products, hand sanitizers, cosmetics and personal care products. It is used to control microbial contamination and has a broad-spectrum of activity against many Gram-positive and Gram-negative bacteria. The development of triclosan tolerance with potential cross resistance to clinically relevant antibiotics in zoonotic pathogens is of concern given the widespread use of this active agent in clinical, food processing and domestic environments. more...

Organism:

Escherichia coli; Escherichia coli O157

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL

(Submitter supplied) Glyphosate is known to inhibit 5-enolpyruvylshikimate-3-phosphate synthase of the chorismate biosynthetic pathway, and chorismate is a precursor to aromatic amino acids, auxin, and many other secondary products. Although the perennial weed leafy spurge (Euphorbia esula L.) is considered glyphosate tolerant, glyphosate is often used as part of an integrated pest management program in non-cultivated ecosystems of North America. more...

Organism:

Euphorbia esula

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18531

8 Samples

Download data: TXT, XLS

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL25406

9 Samples

Download data: PAIR

(Submitter supplied) Bacteria have to continuously adjust to nutrient fluctuations from favorable to less favorable conditions and carbon starvation. The glucose-acetate transition followed by carbon starvation is representative of such carbon fluctuations observed by E. coli in many environments. Regulation of gene expression through fine-tuning of mRNA pools constitutes one of the regulation levels required for such a metabolic adaptation. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL25406

35 Samples

Download data: PAIR

(Submitter supplied) Transcriptional profiling of Escherichia coli TB1 cells under (-)-Roemerine treatment. The genome reprograming in the bacterial cells at transcription level was analyzed through treatment of the bacteria with plant-derived alkaloid, (-)-Roemerine, to elucidate the response of bacteria to the antibacterial drug.

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL13359

13 Samples

Download data: TXT

(Submitter supplied) DNA microarray experiments were used to compare gene expression profiles of untreated and 5-azacytidine treated Escherichia coli at both logarithmic phase and early stationary phase The goal was to determine the effect of cytosine DNA methylation loss on gene expression (5-azacytidine is a methylation inhibitor)

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL13360

10 Samples

Download data: TXT

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

Organism:

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

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL10416 GPL3154

7 Samples

Download data: CEL, PAIR

(Submitter supplied) Chromatin immunoprecipitation was combined with high-density tiling array (ChIP-chip) and gene expression microarray to reveal the adaptive responses of Escherichia coli to phosphate starvation. The first sketch of the genome-wide distribution of PhoB binding profile was unveiled and 43 regions were identified as the PhoB binding regions. The presence of a significant common motif in these binding regions allowed us to reconstruct the PhoB binding pattern. more...

Organism:

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

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL10416

3 Samples

Download data: PAIR

(Submitter supplied) Chromatin immunoprecipitation was combined with high-density tiling array (ChIP-chip) and gene expression microarray to reveal the adaptive responses of Escherichia coli to phosphate starvation. The first sketch of the genome-wide distribution of PhoB binding profile was unveiled and 43 regions were identified as the PhoB binding regions. The presence of a significant common motif in these binding regions allowed us to reconstruct the PhoB binding pattern. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

4 Samples

Download data: CEL

(Submitter supplied) A fermentation strategies with phosphate feeding was applied to elongate transition inti phosphate limitation for an tryptophan overproducing E. coli strain High frequency sampling together with the applied fermentation strategy should provide high resolution insights into regulatory regimes involved in phosphate response

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL3154

10 Samples

Download data: CEL

(Submitter supplied) To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL18948

8 Samples

Download data: TXT

(Submitter supplied) Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material and lack of poly(A)-tails. We described, here, a novel method for single bacterium TTA, using a Burkholderia thailandensis model exposed to subinhibitory concentration of the antibacterial agent, glyphosate. more...

Organism:

Burkholderia thailandensis

Type:

Expression profiling by array

Platform:

GPL7113

3 Samples

Download data: TXT

(Submitter supplied) We investigated the impact of cadmium on the global transcriptome of E. coli wild type, ∆gshA and ∆gshB mutant cells to evaluate the molecular basis of cadmium toxicity in the presence or absence of cellular thiols. This global transcriptome analysis were done with cells synthezising GSH (wild type), gamma-glutamyl-cysteine (∆gshB mutant) or neither of the two cellular thiols (∆gshA mutant) under the influence of 100 µM Cd(II).

Organism:

Escherichia coli; Escherichia coli K-12

Type:

Expression profiling by array

Platform:

GPL534

3 Samples

Download data: TXT

(Submitter supplied) Cellular metabolism controls gene expression through allosteric interactions between metabolites and transcription factors. Methods to detect these regulatory interactions are mostly based on in vitro binding assays, but there are no methods to identify them at a genome-scale in vivo. Here we show that dynamic transcriptome and metabolome data identify metabolites that are potential effectors of transcription factors in E. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26155

56 Samples

Download data: CSV

(Submitter supplied) Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14548

24 Samples

Download data: TXT

(Submitter supplied) To achieve extreme manganese stress, we used DmntP E. coli strain. We identified the pathways that are altered under manganese stress. Mainly, manganese altered the metabolism of iron in the cell. Therefore, we have shown that iron supplementation mitigates manganese toxicity. Overall, our data explains the basis of manganism in higher organisms.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL22574

8 Samples

Download data: TXT

(Submitter supplied) Purpose: The identification of genes and regulatory pathways involved in the susceptibility to ciclopirox activity Methods: mRNA profiles of ciclopirox treatment in wild-type strain using Illumina sequencing. Results: Using an optimized data analysis workflow, we mapped about 1 million sequence reads per sample to the E. coli K-12 genome and identified 4,290 transcripts in wild-type with our without sublethal concentration of ciclopirox (12.5 ug/mL). more...

Organism:

Escherichia coli K-12; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24570 GPL18133

3 Samples

Download data: XLSX

(Submitter supplied) Long-term experiment (150 days) of Escherichia coli MC1000 with daily transfers into fresh LB medium and under three different oxygen regimes.

Organism:

Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL13360

38 Samples

Download data: GPR

(Submitter supplied) We sequenced mRNA of three dual perturbation experiments of E. coli K12 MG1655 changing both genetic and environmental conditions. Each dual perturbation experiment consists of four RNA-seq samples (WT, WT+nutrient supplementation, transcription factor KO, transcription factor KO+nutrient supplementation). The three conditions are: 1) adenine supplementation/nac KO, 2) L-tryptophan supplementation/cra KO, 3) anaerobic/mntR KO.

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16227

14 Samples

Download data: CSV