Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA545093 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
| 2230352 | ecrin-mdr-crc
Project description:Despite the characterization of many aetiologic genetic changes. The specific causative factors in the development of sporadic colorectal cancer remain unclear. This study was performed to detect the possible role of Enteropathogenic Escherichia coli (EPEC) in developing colorectal carcinoma.
| 2184564 | ecrin-mdr-crc
Project description:Intercalated cells are known to be involved in acid-base homeostasis via vacuolar ATPase (H+-ATPase or V-ATPase) expression. Increasing evidence supports an innate immune role for ICs along with their traditional function of pH regulation. In this study, human kidney tissue was enriched for viable intercalated cells then exposed to uropathogenic E. coli versus saline control. Single cell transcriptomics was performed. Six intercalated cell subtypes were identified including hybrid principal-intercalated cells. Cell specific cluster marker gene list generated from this sequencing data was put through ingenuity pathway analysis pipeline which predicted “phagosome maturation” as a key biological pathway that increased in rank following exposure to uropathogenic E. coli in two of the intercalated cell subtypes. Uptake of E. coli and pHrodo coated E. coli BioParticlesTM during live animal intravital microscopy demonstrated that intercalated cell phagocytosis of bacteria was an active process that involved acidification. Taken together, our finding indicate that intercalated cells represent an epithelial cell with characteristics of professional phagocytes like macrophages or neutrophils, which includes the ability to phagocytose E. coli and acidify phagolysosomes.
2020-10-22 | GSE159805 | GEO
Project description:Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.
2015-09-30 | GSE65385 | GEO
Project description:The goal of this study is to compare gene expression data for a well known model organism (Escherichia coli) using different technologies (NGS here, microarray from GSE48776).
2013-07-12 | GSE48829 | GEO
Project description:The aim of the study was to compare the transcriptome of E. coli K12 MG1655 cells lacking hydroperoxidase (Hpx-) and therefore unable to detoxify hydrogen peroxide, to wild-type cells; both when the Rtc RNA repair system is active and when it is inhibited; at 8 and 24 hpi. A very large number of genes (up to 1/3) were found to be differentially expressed in Hpx- as compared to wild-type. Inhibition of the Rtc system had dramatic effects on Hpx- but not on wild-type.
2022-11-02 | GSE165009 | GEO
Project description:We report the effect of oxygenation state in lactose grown escherichia coli producing recombinant proteins. To shed more light on the mechanistic correlation between the uptake of lactose and dissolved oxygen, a comprehensive study has been undertaken with the E. coli BL21 (DE3) strain. Differences in consumption pattern of lactose, metabolites, biomass and product formation due to aerobiosis have been investigated. Transcriptomic profiling of metabolic changes due to aerobic process and microaerobic process during protein formation phase has been studied and the results provide a deeper understanding of protein production in E. coli BL21 (DE3) strains with lactose based promoter expression systems.This study also provides a scientific understanding of escherichia coli metabolism upon oxygen fluctuations.
2020-05-18 | GSE135698 | GEO
Project description: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. Keywords: ChIP-chip
2008-11-19 | GSE11230 | GEO
Project description: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. coli). A dual channel and single channel analysis approach was compared for the comparative genomic hybridization experiments. Moreover, the microarray was used to characterize four unsequenced probiotic E. coli strains, currently marketed for beneficial effects on the human gut flora. Results: Based on the genomes included in this study, we were able to group together 2,041 genes that were present in all 32 genomes. Furthermore, we predict that the size of the E. coli core genome will approach ~1,560 essential genes, considerably less than previous estimates. Although any individual E. coli genome contains between 4,000 and 5,000 genes, we identified more than twice as many (11,872) distinct gene groups in the total gene pool (“pan-genome”) examined for microarray design. Benchmarking of the design based on sequenced control strain samples demonstrated a high sensitivity and relatively low false positive rate. Moreover, the array was highly sufficient to investigate the gene content of apathogenic isolates, despite the strong bias towards pathogenic E. coli strains that have been sequenced so far. Our analysis of four probiotic E. coli strains demonstrate that they share a gene pool very similar to the E. coli K-12 strains but also show significant similarity with enteropathogenic strains. Nonetheless, virulence genes were largely absent. Strain-specific genes found in probiotic E. coli but absent in E. coli K12 were most frequently phage-related genes, transposases and other genes related to mobile DNA, and metabolic enzymes or factors that may offer colonization fitness, which together with their asymptomatic nature may explain their nature. Conclusion: This high-density microarray provides an excellent tool for characterizing either DNA content or gene expression from unknown E. coli strains. Keywords: Comparative genomic hybridizations
2008-01-22 | GSE8595 | GEO