GEO DataSets

(Submitter supplied) The growth of E. coli is inhibited by millimolar concentrations of L-homoserine, which may be problematic for the industrial production of this compound or for products derived from it. In this work, an adapted laboratory evolution (ALE) was applied, which resulted in the isolation of an E. coli strain at least 10-fold more tolerant to L-homoserine than the original (MG1655) strain. Only four genomic modifications were identified after genome sequencing of this evolved strain (designed 4E), including a 49 bp truncation starting from the codon stop of thrL and leading to a modified thrL locus carrying a thrL* allele encoding a 30 amino acids polypeptide, which is 9 amino acids more than the leader peptide encoded by thrL. more...

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

24 Samples

Download data: TXT, XLSX

(Submitter supplied) To compare the transcriptional profiling of a FimZ-expressing strain or non-expressing strain in E. coli under stationary phase. For overexpression of fimZ gene was cloned into pBAD33 plasmid under control of the arabinose-inducible PBAD promoter, which was induced by addition of 0.2% arabinose. Goal was to determine the FimZ regulon in E. coli. Biological replicates: 2 replicates.

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli CFT073; Escherichia coli O157:H7 str. Sakai; Escherichia coli O157:H7 str. EDL933; Escherichia coli BW25113

Type:

Expression profiling by array

Platform:

GPL13359

2 Samples

Download data: TXT

(Submitter supplied) To compare transcriptional profiling of a gadE-, hdeA-, or hdeD- deficient strain to wild type in E. coli under minimum medium conditions. These genes are included in the GAD cluster genes, which are involved in the glutamic acid-dependent acid resistance (GAD) in E. coli. Goal was to determine the GadE, HdeA, or HdeD regulon in E. coli. Biological replicates: 2 replicates.

Organism:

Escherichia coli BW25113; 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

6 Samples

Download data: TXT

(Submitter supplied) The function of cvpA, a bacterial gene predicted to encode an inner membrane protein, is largely unknown. Early studies in E. coli linked cvpA to Colicin V secretion and recent work revealed that it is required for robust intestinal colonization by diverse enteric pathogens. In enterohemorrhagic E. coli (EHEC), cvpA is required for resistance to the bile salt deoxycholate (DOC). Here, we carried out genome-scale transposon-insertion mutagenesis and spontaneous suppressor analysis to uncover cvpA’s genetic interactions and identify common pathways that rescue the sensitivity of a ∆cvpA EHEC mutant to DOC. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Other

Platform:

GPL23073

6 Samples

Download data: TXT

(Submitter supplied) sRNAs play important roles in regulating gene expression post-transcriptionally. Here, we used RNA-seq to compare gene expression in a WT strain and a dicF1-4 deletion strain.

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24005

6 Samples

Download data: TXT

(Submitter supplied) Pathogens like E. coli O157:H7 are responsible for many outbreaks and can be found and survive in poor inorganic phosphate (Pi) environments. In E. coli the phosphate homeostasis is regulated by the Pst system and the two-component system PhoB/R. In a Δpst mutant, PhoB is constitutively activated and biofilm formation is increased. To understand how PhoB activation lead to biofilm increase, we compared the transcriptomes of EDL933 the WT strain and Δpst mutant both grown in MOPS Pi rich medium, using the Affymetrix GeneChip® E. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL3154

6 Samples

Download data: CEL

(Submitter supplied) We found that nemerous genes were up- or down regulated in ∆dnaK, including RpoS-regulated genes.

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

4 Samples

Download data: TXT

(Submitter supplied) E. coli (P1645ec: a clinical isolate) was incubated with differing concentrations of antimicrobial peptides (all at 0.5X MBC)

Organism:

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

Type:

Expression profiling by array

Platform:

GPL13359

8 Samples

Download data: TXT

(Submitter supplied) APEC cause avian colibacillosis in poultry, characterized by the systematic infection, such as septicemia, airsacculitis, and pericarditis. APEC mainly use two-component regulatory systems (TCSs) to deal with the stressing environments in host during their infection. Whereas most TCSs in E.coli are well characterized, the characterization of RstA/RstB in APEC has not been thoroughly investigated. To understand the whole picture of RstA/RstB regulation, especially its role in virulence regulation, transcriptional analysis of the effect of rstAB deletion was performed in vivo. more...

Organism:

Escherichia coli CFT073; Escherichia coli O157:H7 str. EDL933; Escherichia coli O157:H7 str. Sakai; Escherichia coli APEC O2; Escherichia coli str. K-12 substr. MG1655

Type:

Expression profiling by array

Platform:

GPL13359

6 Samples

Download data: TXT

(Submitter supplied) Enteric pathogens with low infectious doses rely on the ability to orchestrate expression of virulence and metabolism-associated genes in response to environmental cues for successful infection. Accordingly, the human pathogen enterohemorrhagic Escherichia coli (EHEC) employs a complex multifaceted regulatory network to link expression of type III secretion system (T3SS) factors to nutrient availability. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24005

6 Samples

Download data: TXT

(Submitter supplied) We conducted comparative gene co-expression network (GCN) analyses of two O113:H21 STEC strains: EH41, reference strain, isolated from hemolytic-uremic syndrome patient in Australia, and Ec472/01, isolated from cattle feces in Brazil. These strains were cultured in fresh or in Caco-2 cell conditioned media. GCN analyses were also accomplished for cultured Caco-2 cells exposed to EH41 or Ec472/01. Differential transcriptome profiles for EH41 and Ec472/01 were not significantly changed by exposure to fresh or Caco-2 conditioned media. more...

Organism:

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

Type:

Expression profiling by array

Platforms:

GPL13359 GPL6480

32 Samples

Download data: TXT

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

Organism:

Escherichia coli CFT073; Escherichia coli O157:H7 str. EDL933; Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S; Escherichia coli str. K-12 substr. MG1655; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array

Platforms:

GPL24239 GPL13359

19 Samples

Download data: TXT

(Submitter supplied) In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in E. coli responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. more...

Organism:

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

Type:

Expression profiling by array

Platform:

GPL13359

11 Samples

Download data: TXT, XLSX

(Submitter supplied) Transcriptional analysis of rpoC K370_A396dup mutants for tolerance to sodium chloride

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

8 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of mid-log phase (OD600 ~ 0.8) E. coli BW25113 cells grown treated with 2 mM NaN3 for 10 minutes

Organism:

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

Type:

Expression profiling by array

Platform:

GPL13360

2 Samples

Download data: TXT

(Submitter supplied) The microarray study was used to compare the gene expression profile of EDL933 in LB, sdhA deletion mutant in LB, and sdhA deletion mutant in LB with 2.5 mM Fumaric acid.

Organism:

Escherichia coli O157:H7 str. EDL933; Escherichia coli O157:H7

Type:

Expression profiling by array

Platform:

GPL22407

8 Samples

Download data: TXT

(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) The present study examines changes in global gene expression patterns and in virulence factor-associated genes in an extended spectrum beta-lactamase (ESBL)-producing UPEC (ESBL019) during the morphologic transitions induced by an ineffective antibiotic and in the presence of human primary bladder epithelial cells. The morphological shifts induced by ineffective antibiotics are associated with significant transcriptional virulence alterations in ESBL-producing UPEC, which may affect survival and persistence in the urinary tract.

Organism:

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

Type:

Expression profiling by array

Platform:

GPL13359

16 Samples

Download data: TXT

(Submitter supplied) While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL23073

4 Samples

Download data: XLSX

(Submitter supplied) Global response to ciprofloxacin in low level quinolone resistant Escherichia coli: a shorter path to survival. Background: Bactericidal activity of quinolones in bacteria has been related to a combination of DNA fragmentation, ROS production and programmed dead cell systems. Subjacent molecular systems responsible for reduction of bactericidal effect in low-level quinolone resistance (LLQR) phenotypes remain to be clarified. more...

Organism:

Escherichia coli O157:H7 str. EDL933; Escherichia coli CFT073; Escherichia coli str. K-12 substr. MG1655; Escherichia coli ATCC 25922; Escherichia coli O157:H7 str. Sakai

Type:

Expression profiling by array

Platform:

GPL13360

8 Samples

Download data: TXT, XLSX