GEO DataSets

(Submitter supplied) The existence of two separate lineages of Escherichia coli O157:H7 has previously been reported, and research indicates that one of these lineages (lineage I) might be more pathogenic towards human hosts. We have previously shown that the more pathogenic lineage expresses higher levels of Shiga toxin 2 (Stx2) than the non-pathogenic lineage II. To evaluate why lineage 2 isolates do not express appreciable levels of toxin, two lineage 2 isolates (FRIK966 and FRIK2000) were chosen as representatives of lineage 2 and whole genome microarrays were performed using Agilent microarrays using the E. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL8845

8 Samples

Download data: GPR

(Submitter supplied) Two outbreak strains of E. coli O157:H7 differ phylogenetically, in gene content, and in epidemiological characteristics. The working hypothesis in this experiment was that these strains will also differ in the transcription of shared virulence genes. Indeed, following a 30 minute exposure to epithelial cells, strain TW14359 overexpressed major and ancillary virulence genes, relative to strain Sakai.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL7445

1 Sample

Download data: GPR

(Submitter supplied) Transcriptomes of 24 clinical strains of E. coli O157:H7 that differ phylogenetically and by Shiga toxin profiles were compared after 30 min co-incubation with epithelial cells.

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL7445

36 Samples

Download data: GPR

(Submitter supplied) The transcriptome of Escherichia coli K-12 has been widely studied over a variety of conditions for the past decade while such studies involving E. coli O157:H7, its pathogenic cousin, are just now being conducted. To better understand the impact of intracellular life within a ruminant and environmental protozoan on E. coli O157:H7, global transcript levels of strain EDL933 cells inside Acanthamoeba were compared to cell grown in the protozoan media (ATCC PYG712) by microarray.

Organism:

Escherichia coli O157:H7 str. EDL933; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL6272

9 Samples

Download data: TXT

(Submitter supplied) Effect of human macrophages phagocytosis on the global transcriptome of EDL933 at different time. Infection of THP-1 with EDL933. Application of SCOTS technique to have cDNA. Hybridation on microarray. Reference: EDL933 in RPMI medium Keywords: stres response, host-bacteria response, time-course

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL6178

16 Samples

Download data

(Submitter supplied) epoxide coated Protocol: Using the transcriptome of E. coli O157:H7 EDL933 an oligonucleotide microarray, made up of 43-45 mers, was designed. Based upon available funding we were able to choose 610 genes originally, in the current submission 2 additional genes were added for a total of 612 genes [see Additional file 1] (including 10 negative control genes derived from pig EST sequences). The genes on the O157 array were selected based upon their being associated with virulence or with regulation of virulence genes. more...

Organism:

Escherichia coli O157:H7 str. EDL933

Download data: GAL

(Submitter supplied) Escherichia coli O157:H7 strains have been classified into different genotypes based on the presence of specific shiga toxin-encoding bacteriophage insertion sites. Genotypes that are predominant in clinical isolates are named clinical genotypes and those that are isolated mostly from bovine sources are bovine-biased genotypes. To determine whether inherent differences in gene expression could possibly explain the variation in infectivity of these genotypes, we compared the expression patterns of O157:H7 strains isolated from cattle, which belonged to either clinical genotype 1 or bovine-biased genotype 5. more...

Organism:

Escherichia coli

Type:

Expression profiling by array

Platform:

GPL7445

16 Samples

Download data: GPR

(Submitter supplied) We describe the design and evaluate the use of a high density oligonuclotide microarray covering seven sequenced E. coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. more...

Organism:

Escherichia coli

Type:

Genome variation profiling by array

Platform:

GPL3680

14 Samples

Download data: CEL

(Submitter supplied) Background: Enterohemorrhagic Escherichia coli (EHEC) O157 causes severe food-bone illness in humans. The chromosome of O157 consists of 4.1-Mb backbone sequences shared by benign E. coli K-12, and 1.4-Mb O157-specific sequences encoding many virulence determinants such as Shiga toxin genes (stxs) and the locus of enterocyte effacement (LEE). Non-O157 EHECs belonging to clonal lineages distinct from O157 also cause similar illness in humans. more...

Organism:

Escherichia coli

Type:

Genome variation profiling by array

Platform:

GPL5329

56 Samples

Download data: TXT

(Submitter supplied) This study characterises large chromosomal rearrangements (LCRs) and their associated phenotypes in E. coli O157 strains. RNA-seq was performed on wildtype strain 9000 and three derivative strains in which LCRs had occurred following experimental bovine colonisation. Gene expression differences between these strains was analysed when each was grown in either LB or M9 media.

Organism:

Escherichia coli O157

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29209

24 Samples

Download data: GTF, TAB

(Submitter supplied) RpoS is a conserved stress regulator that plays a critical role in survival under stress conditions in Escherichia coli and other γ-proteobacteria. RpoS is also involved in virulence of many pathogens including Salmonella and Vibrio species. Though well characterized in non-pathogenic E. coli K12 strains, the effect of RpoS on transcriptome expression has not been examined in pathogenic isolates. E. more...

Organism:

Escherichia coli; Escherichia coli O157:H7 str. EDL933

Type:

Expression profiling by array

Platform:

GPL3154

12 Samples

Download data: CEL

(Submitter supplied) The high frequency of prophage insertions in the mlrA gene of clinical serotype O157:H7 isolates renders such strains deficient in csgD-dependent biofilm formation but prophage induction may restore certain mlrA properties. In this study we used transcriptomics to study the effect of high and low sulfamethoxazole–trimethoprim (SMX-TM) concentrations on prophage induction, biofilm regulation, and virulence gene expression in strain PA20 under environmental conditions following five-hour and 12-hour exposures. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18133

18 Samples

Download data: CSV

(Submitter supplied) Curli are adhesive fimbriae of Enterobactericaeae and are involved in surface attachment, cell aggregation and biofilm formation. We previously reported that natural curli variants of E. coli O157:H7 (EcO157) displayed distinct acid resistance; however, this difference was not linked to the curli fimbriae per se. Here, we investigated the underlying molecular basis of this phenotypic divergence between the curli variants. more...

Organism:

Escherichia coli; Escherichia coli O157:H7

Type:

Expression profiling by array

Platform:

GPL14768

30 Samples

Download data: TXT

(Submitter supplied) 60-mers oligonucleotide probes, in-situ synthesis on 1 Protocol: Sure Print Technology-In situ synthesis

Organism:

Staphylococcus aureus

4 Series

30 Samples

Download data

(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) Background: Based on 32 Escherichia coli and Shigella genome sequences, we have developed an E. coli pan-genome microarray. Publicly available genomes were annotated in a consistent manor to define all currently known genes potentially present in the species. The chip design was evaluated by hybridization of DNA from two sequenced E. coli strains, K-12 MG1655 (a commensal) and O157:H7 EDL933 (an enterotoxigenic E. more...

Organism:

Escherichia coli

Type:

Genome variation profiling by array

Platform:

GPL5647

10 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

20 Samples

Download data: CEL

(Submitter supplied) A huge number of microorganisms are colonized in human gut and the balance of their composition is closely related to human health. Recently, many probiotics such as bifidobacteria or lactobacilli have been introduced in our life as effective agents. However, we have not well understood their beneficial mechanisms including host-bacterial crosstalk. Accordingly, we took advantage of the protective mechanisms of probiotics against lethal infection of enterohemorrhagic Escherichia coli O157:H7 in murine gnotobiote model system

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

14 Samples

Download data: CEL

(Submitter supplied) A huge number of microorganisms are colonized in human gut and the balance of their composition is closely related to human health. Recently, many probiotics such as bifidobacteria or lactobacilli have been introduced in our life as effective agents. However, we have not well understood their beneficial mechanisms including host-bacterial crosstalk To analyze the differences of gene expression between BA- or BL-associated murine colonic epithelium, we performed comparative transcriptomic analysis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Transcriptome profiling of E. coli MG1655, E. coli EDL933, E. coli ECOR26, and E. coli Nissle 1917 grown on mouse cecal mucus as carbon source The carbon sources that support growth of pathogenic E. coli O157:H7 in the mammalian intestine have not previously been investigated. In vivo, pathogenic E. coli EDL933 primarily grows as dispersed single cells within the mucus layer that overlies the mouse cecal epithelium. more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Bacillus anthracis; Escherichia coli CFT073; Bacteroides thetaiotaomicron VPI-5482; Escherichia coli O157:H7 str. Sakai; Escherichia coli; Escherichia coli O157:H7 str. EDL933; Enterococcus faecalis V583; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Type:

Expression profiling by array

Platform:

GPL6702

16 Samples

Download data: CEL, TXT