Project description:We used RNA-seq to profile transcriptomic changes underlying the phenotypic variations observed between E. coli strains expressing different RpoD ortholog variants.
Project description:Genotyping of RpoD mutants via amplicon sequencing from the following manuscript: \\"Systematic dissection of σ70 sequence diversity and function in bacteria\\" by Park and Wang (2020). Includes raw sequencing reads from samples from MAGE-seq single codon saturation mutagenesis and high-throughput fitness competition experiment as well as the RpoD ortholog mutants generated through recombineering and CRISPR selection.
Project description:Characterization of a metagenomic regulatory sequence library derived from M. xanthus, E. coli, and O. urethralis genomes in strains expressing different RpoD ortholog variants. Targeted DNA and RNA seq used to profile relative DNA and RNA abundances, respectively of each regulatory sequence construct in the library.
Project description:ChIP-on-chip analysis of RNAP and RpoD binding to the Salmonella enterica serovar Typhimurium chromosome demonstrated a high degree of overlap between RNAP and RpoD binding and provided us with important insights into the global distribution of these factors. Furthermore this data was correlated with information on the location of 1873 transcription start sites identified by RNA-Seq technology, thereby providing a detailed transcriptional map of Salmonella Typhimurium. Analysis of RNAP, RNAP-Rifampicin and and RpoD binding in Luria Broth (LB)
Project description:We report RNA-seq data for four Pseudomonas fluorescens SBW25 types: SBW25 (wild type) and dervied types 6A4, 6B4-Cap- and 6B4-Cap+. The aim of the study is to see the effect of a mutation in rpoD (carried by 6B4) on the transcriptome.
Project description:ChIP-on-chip analysis of RNAP and RpoD binding to the Salmonella enterica serovar Typhimurium chromosome demonstrated a high degree of overlap between RNAP and RpoD binding and provided us with important insights into the global distribution of these factors. Furthermore this data was correlated with information on the location of 1873 transcription start sites identified by RNA-Seq technology, thereby providing a detailed transcriptional map of Salmonella Typhimurium.
Project description:Time course experiment to analyze transcriptional changes to the E. coli transcriptome due to overexpressing the heterologous sigma70 factor (RpoD) of Lactobacillus plantarum. A plasmid control strain (pControl) and the sigma70 overexpression strain (pLPLσ) were cultivated in parallel and after induction of RpoD expression samples for transcriptional profiling were taken in exponential, transition and stationary phase.
Project description:We applied a ChIP-chip approach to elucidate the binding profiles of RNAP and RpoD experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays.
Project description:We applied a ChIP-chip approach to elucidate the binding profiles of RNAP and RpoD experimentally under different growth conditions. This technique localizes DNA fragments within DNA-protein complexes enriched by chromatin immunoprecipitation using high-density oligonucleotide tilling arrays. A 21 ChIP-chip study using immunoprecipitated DNA (IP-DNA) from three culture conditions for RNAP and four culture conditions for RpoD. The high-density oligonucleotide tiling arrays used consisted of 381,174 oligonucleotide probes spaced 20 bp apart (30-bp overlap between two probes) across the G. sulfurreducens genome (NimbleGen). Experiments were conducted as three bioliogical replicates (different cultures).