Project description:Whole genome analysis of gene expression by Pectobacterium atrosepticum strain SCRI1043 wildtype and its relA, expI and rpoS deletion mutants when grown to exponential and stationary phase in PMB media. The data is further described in Bowden et al (2013) Virulence in Pectobacterium atrosepticum is regulated by a coincidence circuit involving quorum sensing and the stress alarmone, (p)ppGpp. Molecular Microbiology. DOI: 10.1111/mmi.12369
Project description:HexA is a global transcriptional regulator involved in quorum sensing and virulence regulation in Pectobacterium carotovorum PCC27. To identify genome-wide DNA binding sites of HexA, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using a FLAG-tagged HexA strain. Samples were collected at two different growth phases—mid-log and early stationary—to investigate condition-dependent differences in HexA binding profiles. A total of six samples (three biological replicates per condition) were sequenced on the Illumina NovaSeq 6000 platform using paired-end 101 bp reads. Peaks were called using MACS2, and downstream analysis was performed with ChIPseeker. This study provides insight into the dynamic regulation of HexA across bacterial growth stages.
Project description:Whole genome analysis of gene expression by Pectobacterium atrosepticum strain SCRI1043 wildtype and its relA, expI and rpoS deletion mutants when grown to exponential and stationary phase in PMB media. The data is further described in Bowden et al (2013) Virulence in Pectobacterium atrosepticum is regulated by a coincidence circuit involving quorum sensing and the stress alarmone, (p)ppGpp. Molecular Microbiology. DOI: 10.1111/mmi.12369 A 24 chip study using total RNA recovered from three separate wild-type cultures of Pectobacterium atrosepticum SCRI1043 and three separate cultures from three single mutant strains of SCRI1043 possessing deletions within relA (ECA3569), expI (ECA0105) or rpoS (ECA3530) when grown in Pel Minimal Broth (PMB) media to log-phase (6h) or early stationary phase (14h) growth. Each chip measures the expression level of 4,472 genes from Pectobacterium atrosepticum SCRI1043 with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.