ABSTRACT: HilD is a regulator of Salmonella pathogenicity island 1 (SPI-1) virulence genes in Salmonella enterica serovar Typhimurium. To identify novel HilD-regulated genes, we mapped the genome-wide association of HilD in S. Typhimurium under SPI-1-inducing conditions (high salt, low aeration) using ChIP-seq. HilD was C-terminally tagged with 3 FLAG tags in strain 14028s.
INSTRUMENT(S): Helicos
ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu
Project description:To generate and compile data from ChIP-Seq libraries. Looking at genome-wide binding of transcription factors HilD, HilC, RtsA, RtsB, SprB, and InvF under SPI-1 inducing growth conditions in duplicate.
Project description:FliA in S. Typhimurium directs transcription of large numbers of unstable, non-coding RNAs from intragenic promoters. Also in this study, we identify two previously unreported FliA-transcribed protein coding genes, including sdiA, which encodes a transcription factor that responds to quorum sensing signals produced by other bacteria.
Project description:ChIP-seq was performed to map the association of SPA-tagged DnaA across the Escherichia coli MG1655 chromosome during exponential phase growth in LB. As a control to remove background, ChIP-Seq was also performed on SPA-tagged AcpS, a protein that is not known to bind DNA.
Project description:To determine sites where RpoS binds (and hence likely plays a direct role in transcription), we used ChIP-seq to map the association of RpoS across the Escherichia coli chromosome during stationary phase growth in minimal medium. To facilitate ChIP, RpoS was C-terminally SPA-tagged at its native locus.
Project description:We performed ChIP-seq analyses of RhlR to map the C4-homoserine lactone-dependent and PqsE-dependent RhlR binding sites in the P. aeruginosa genome.
Project description:We used ChIP-seq to map binding of the CRISPR surveillance complex, Cascade, in an E. coli strain lacking the endonuclease Cas3. These data enabled us to determine the precise sequence requirements for Cascade binding.
Project description:To generate and compile data from ChIP-Seq libraries. Looking at CRP, H-NS, and sigma70 binding genome wide under M9 minimal growth conditions in duplicate.
Project description:We mapped the genome-wide binding of the flagellar regulators FlhD, FlhC, and FliA in FLAG-tagged derivatives of E. coli K-12 MG1655 using ChIP coupled with deep sequencing (ChIP-seq). We identify new binding sites for each factor.
Project description:We mapped the genome-wide binding of C-terminally FLAG-tagged AraC in S. enterica subsp. enterica serovar Typhimurium strain 14028s using ChIP coupled with deep sequencing (ChIP-seq). We identified five putative target loci for AraC: upstream of araB/araC, araE, araJ, STM14_0178, and within sseD.