Project description:This research focuses on the design, manufacturing and validation of a new E. coli whole-genome tiling micraorray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The E. coli MG1655 genome is re-acquired with next-generation sequencing and then used to design the tiling microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting E. coli under various growth conditions and then using the tiling microarrays to verify expected gene expression patterns.
Project description:Transcriptional profiling of E. coli cells comparing control harboring the empty vector pRadGro (Ec-pR) with E. coli expressing the Deinococcus radiodurans response regulator DR1558 (Ec-1558) Expression of DR1558 conferred to multi-stress tolerance to E. coli.
Project description:Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR.
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ∆hns/∆stpA strain from exponental growth under aerobic and anaerobic growth conditions. The results are further described in the article Genome-scale Analysis of E.coli FNR Reveals the Complex Features of Transcrtipion Factor Binding.
