Project description:To get a global view of PT modification’s function in ∆dam mutant, we did an RNA-seq to compare the gene expression change after dam knocks out and test whether PT could restore the changes.
Project description:To determine the transcription start site and the abundance of dam mRNA, we conducted mRNA-specific RNA-Seq experiments. Essentially two strategies were tested. First strategy: We obtained the cDNA with a specific RT-PCR in order to get the mRNA from our dam construct (see DNA-seq of DamID reporter cassette). An enrichment, in which we used a Biotinylated dam oligo and Streptavidin magnetic beads, was needed. Then, similar to SHAPE-seq, the ssDNA ligation was performed with CircLigase. The last step was the PCR reaction in order to prepare the cDNA libraries to be sequenced. Second strategy: Similar to the first one, but the specificity was introduced at the PCR, not at the RT. Thereby, busk cDNA was prepared with random hexamers. The enrichment step was not needed.
Project description:The goal of the study is to obtain rna concentrations of E.coli under different growth conditions including growth phase carbon source and salt stresses of Mg+2 and Na+
Project description:Transcriptional profiling of E.coli SE15 comparing wild type E.coli SE15 with Autoindecur 2 synthesis gene LuxS mutnat E.coli SE15. E.coli SE15 is isolated from indwelling catheter of urinary tract infected patient. Examine change of quorum sensing related gene by deleting autoinducer 2 synthesis gene LuxS in E.coli
Project description:We determined the global gene expression profiles of wildtype, dam, dam mutS, and mutS mutant E. coli strains. Keywords: Basal gene expression comparison
Project description:We have estimated the fitness effects of horizontally transferred Salmonella genes to E.coli. To better understand the role of protein-protein interactions, we want to identify the expression levels of known interaction partners of the transferred genes.