Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1051772 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Comparative genome hybridization of transconjugants of E. faecalis OG1RF mated with V583. The total DNA of transconjugants was compared with wildtype strains to ascertain the amount of DNA that was transferred from E. faecalis V583 to E. faecalis OG1RF.
2009-05-08 | E-MEXP-2135 | biostudies-arrayexpress
Project description:In this study transcriptional start sites (TSS) of E. coli were determined for several growth conditions To detect the complement of transcripts expressed from E. coli, we collected two independent biological replicates (B1 and B2 samples) from MG1655 wild type strain grown to exponential (OD 600 ~0.4) or stationary phase (OD 600 ~2.0) in LB medium (samples LB 0.4 and LB 2.0, respectively) as well as grown to exponential phase (OD 600 ~0.4) in M63 minimal glucose medium (sample M63 0.4). For all six samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5M-bM-^@M-^Y terminator exonuclease (+TEX samples), which degrades RNAs containing a 5M-bM-^@M-^Y-mono-phosphate (5M-bM-^@M-^Y-P) and, thus, enriching enriches for primary transcripts containing 5M-bM-^@M-^Y-tri-phosphates (5M-bM-^@M-^Y-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5M-bM-^@M-^Y-PPP) and processed RNAs (5M-bM-^@M-^Y-P).
2014-10-18 | E-GEOD-55199 | biostudies-arrayexpress
Project description:We investigated a paradoxical re-growth of E. coli upon treatment of a novel siderophore-conjugate, LP-600, at concentrations 16-32 times above the minimum inhibitory concentration (MIC).Transcriptome analysis revealed that LP-600 induced the expression of genes involved in SOS response and e14 prophage upon regrowth conditions.
2022-07-31 | GSE197880 | GEO
Project description:Complete squence of Escherichia coli FXCREC123 containing blaNDM-67
| PRJNA1290836 | ENA
Project description:Complete squence of Escherichia coli FXCREC180 containing blaNDM-68
| PRJNA1290869 | ENA
Project description:To assess the degree of transcription in E.coli of ectopic DNA from related gamma proteobacteria, we designed a custom NimbleGen array containing highly redundant and substantially complete oligonucleotide probe sets for E. coli, H. influenzae and P. aeruginosa annotated genes. We transformed E. coli, in separate experiments, with individual BAC clones and probed arrays with cDNA derived from DNase treated RNA isolated from the overnight culture of the transformants. Keywords: cross-regulation on genomic scale
2008-04-05 | GSE11051 | GEO
Project description:<p>Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes. We made predictions of the etiology of disease in individual subjects based on the properties and features of the recovered cellular genomes. Three subtypes of samples were observed. First were four patients with low diversity metagenomes that were predominated by one or more pathogenic E. coli strains. Annotation allowed prediction of pathogenic type in most cases. Second, five patients were co-infected with E. coli and other members of the Enterobacteriaceae, including antibiotic resistant Enterobacter, Klebsiella, and Citrobacter. Finally, several samples contained genomes that represented dark matter. In one of these samples we identified a TM7 genome that phylogenetically clustered with a strain isolated from wastewater and carries genes encoding potential virulence factors. We also observed a very high proportion of bacteriophage reads in some samples. The relative abundance of phage was significantly higher in healthy travelers when compared to TD patients. Our results highlight that assembly-based analysis revealed that diarrhea is often polymicrobial and includes members of the Enterobacteriaceae not normally associated with TD and have implicated a new member of the TM7 phylum as a potential player in diarrheal disease. </p>
| phs001352 | dbGaP