Project description:Investigation of whole genome gene expression level changes in a Vibrio cholerae O395N1 delta-nqrA-F mutant, compared to the wild-type strain. Total RNA recovered from wild-type cultures of VIbrio cholerae O395N1 and its nqrA-F mutant strain. Each chip measures the expression level of 3,835 genes from Vibrio cholerae O1 biovar eltor str. N16961 with twenty average probes/gene, with five-fold technical redundancy.
Project description:Temperature is a crucial environmental signal that govers the occurrence of Vibrio cholerae and cholera outbreaks. To understand how temperature impacts the transcriptome of V. cholerae we performed whole-genome level transcriptional profiling using custom microarrays on cells grown at human body temperature (37 C) then shifted to temperatures V. cholerae experience in the environment (15 C and 25 C). Overall design: Wild-type V. cholerae grown at 37 C were compared to those shifted to either 15 C or 25 C. Threee biological replicates were performed for each condition. All reference RNA was harvested from a wild-type strain grown at 30 C.
Project description:Environmental isolates of Vibrio cholerae from California coastal water compared to reference strain N16961. A genotyping experiment design type classifies an individual or group of individuals on the basis of alleles, haplotypes, SNP's. Keywords: genotyping_design; array CGH Overall design: User Defined
Project description:To gain an insight into the changes between CTX-positive and -negative strain, apart from the CTX phage deletion, we carried out microarray analysis and whole genome sequencing of both strains Overall design: Organism : Vibrio cholerae, Agilent's V.cholerae GXP Expression 8x15k Array (AMADID: 022386) desined by Genotypic Technology, Bangalore
Project description:This study is an analysis of changes in gene expression during stringent response in Vibrio cholerae. V. cholerae cells in mid-log were treated with serine hydroxamate and gene expression was compared to untreated cells. Keywords: Stress response, stringent response Overall design: V. cholerae cells in mid-log were treated with the stringent response inducer serine hydroxamate for one doubling time, then RNA was harvested using a Trizol method. Mock-treated cells (V. cholerae with dH2O added) also had RNA harvested. Both serine-hydroxamate treated and wild type cell RNA was converted to cDNA, with one set incorporating Cy5, the other Cy3, with fluorophores reversed in the multiple analyses. RNA from both conditions was applied to a whole genome PCR microarray from V. cholerae N16961, containing two sets of every ORF. Data was analyzed by Genepix and Rosetta Resolver.
Project description:Question Addressed: What is the level of expression of genes in Vibrio cholerae recovered from various conditions. These conditions include samples recovered directly from patients (O139 from stool samples from ICDDR,B and N16961 from stool samples from a vaccine trial held in Cincinnati) as well as standard logarithmic and stationary phase grown bacteria. Labeling reactions were performed in duplicate for each stool derived and in quadruplicate for each in vitro grown strain. A common reference was used for each slide, it was composed of RNA from the exponentially growing 92A1552 V. cholerae strain transcription profiling by array
Project description:Lon protease is known to regulate various transcriptional regulators in other bacterial organisms. To understand whether lon protease is involved in transcriptional changes in Vibrio cholerae, wholel-genome level transcriptional profiling was performed using custom microarrays. Transcriptomes of lonA mutant and wild-type strains were compared in this study. Three biological replicates of wild-type and lonA mutant strains were used for this study. Reference RNA sample was harvested from wild-type strain.
Project description:DNA methylation is a key epigenetic regulator in all domains of life, yet the effects of most bacterial DNA methyltransferases on cellular processes are largely undefined. Here, we used diverse techniques, including bisulfite sequencing, transcriptomics, and transposon insertion site sequencing to extensively characterize a 5-methylcytosine (5mC) methyltransferase, VchM, in the cholera pathogen, Vibrio cholerae. We have comprehensively defined VchM's DNA targets, its genetic interactions and the gene networks that it regulates. Although VchM is a relatively new component of the V. cholerae genome, it is required for optimal V. cholerae growth in vitro and during infection. Unexpectedly, the usually essential σE cell envelope stress pathway is dispensable in ΔvchM V. cholerae, likely due to its lower activation in this mutant and the capacity for VchM methylation to limit expression of some cell envelope modifying genes. Our work illuminates how an acquired DNA methyltransferase can become integrated within complex cell circuits to control critical housekeeping processes. Duplicates were used for all samples. For each strain background (C6706 and O395), there were control (Wildtype) samples and experimental samples (VchM knockout)
Project description:The experiment contains ChIP-seq data for Vibrio cholerae strain E7946. The strain was grown at 37 degrees in LB medium and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.