Project description:RNA sequencing of Escherichia coli Nissle 1917 before and after HOCl treatment was perfomed to identify pathways that may be important in responding to oxidative stress caused by reachive chlorine species (RCS).
Project description:This study used prokaryotic strand-specific RNA sequencing to characterize transcriptomic changes associated with knockout of two global transcriptional regulator genes, cra and crp, encoding catabolite repressor/activator (CRA) and cAMP receptor protein (CRP), respectively, in Escherichia coli Nissle 1917. Four genotypes were profiled: wild-type strain, delta_cra mutant, delta_crp mutant, and delta_cra_delta_crp double-knockout mutant. Cells were cultured in MS medium and harvested at OD600 = 0.6. Ribosomal RNA was depleted, strand-specific RNA-seq libraries were constructed, and paired-end sequencing reads were generated on an Illumina NovaSeq 6000 platform. Gene-level read count, RPKM, and TPM matrices were generated to compare expression profiles among genotypes.
Project description:To determine whether calprotectin can elicit any transcriptional response in the probiotic E. coli Nissle 1917(EcN), EcN was treated with 200 ug/g of calprotectin in log phase.
