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GenomicsLoRTIS: A long read method for analysis of large transposon mutant libraries
Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the re...
ORGANISM(S): Escherichia coli BW25113 
2022-05-30 | E-MTAB-11351 | biostudies-arrayexpress
TranscriptomicsWhole genome \"TraDIS-Xpress\" assay to determine gene roles during growth of E. coli in different concentrations of the antibiotics trimethoprim and sulfamethoxazole
To assay every gene in the E. coli genome to identify those that contribute to increased or decreased susceptibility to the antibiotics trimethoprim and sulfamethoxazole. This will help to define more accurately those bacterial cell mechanisms that contribute to these phenomena and provide informat...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2020-10-19 | E-MTAB-9305 | biostudies-arrayexpress
GenomicsTraDIS-Xpress analysis of colistin stress responses in Escherichia coli
In past, resistance mechanisms have been identified by analysis of resistant isolates or defined mutants. Recently, high-throughput transposon mutagenesis coupled with sequencing (TraDIS-Xpress) is another approach proving useful for elucidating the roles of genes involved in the overall cellular re...
ORGANISM(S): Escherichia coli BW25113 
2022-06-09 | E-MTAB-11807 | biostudies-arrayexpress
GenomicsTraDIS-Xpress analysis of gene functions in Escherichia coli
This experiment was conducted to understand the gene functions of Escherichia coli in different concentrations of induction of Isopropyl β-D-1-thiogalactopyranoside (IPTG). Experiments were performed with no induction, or with induction using 0.2mM or 1 mM of IPTG.
ORGANISM(S): Escherichia coli BW25113 
2022-06-09 | E-MTAB-11808 | biostudies-arrayexpress
GenomicsPrior exposure strongly influences mechanisms underpinning survival of heat shock in Escherichia coli
In past, heat stress mechanisms have been identified by analysis of RNA-seq or proteomics. Recently, high-throughput transposon mutagenesis coupled with sequencing (TraDIS-Xpress) is another approach proving useful for elucidating the roles of genes involved in the overall cellular response to a par...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2026-05-29 | E-MTAB-15219 | biostudies-arrayexpress
UnknownSubgenomic sequence analysis reveals emergence of new circulating recombinant forms of HIV-1 in Pakistan.
Not available
S-EPMC9532646 | biostudies-literature
GenomicsHigh resolution chemical-genomics identifies targets for synergistic antibiotics with aztreonam
A whole genome screen was used to assay every gene of Escherichia coli strain BW25113 to identify genes involved in susceptibility to the monobactam (beta-lactam) antibiotic aztreonam. The methodology has been called TraDIS-Xpress, and is a version of TraDIS or Tn-seq. A transposon mutant library c...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2024-07-06 | E-MTAB-11576 | biostudies-arrayexpress
UnknownInsights into genome evolution, pan-genome, and phylogenetic implication through mitochondrial genome sequence of Naegleria fowleri species.
Not available
S-EPMC9339544 | biostudies-literature
GenomicsWhole genome TraDIS-Xpress assay to determine gene roles during growth of E. coli in different concentrations of the beta-lactam antibiotic meropenem
The aim of the experiment was to assay every gene in the E. coli genome to identify those that contribute to increased or decreased susceptibility to the beta-lactam antibiotic meropenem. A library of transposon-insertion mutants was grown overnight in the presence or absence of a range of concentra...
ORGANISM(S): Escherichia coli K-12 
2022-06-09 | E-MTAB-11802 | biostudies-arrayexpress
UnknownFrequency and predictors of non-adherence to lifestyle modifications and medications after coronary artery bypass grafting: A cross-sectional study.
Not available
S-EPMC5560880 | biostudies-literature
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