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: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: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: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:Tissue Transcriptomics of mice at different stages of Vibrio cholerae infection and possible RNA-Seq of Vibrio cholerae at the same time pointsThese data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
Project description:Blue light (BL) is a major environmental factor that affects the physiology, behavior, and infectivity of bacteria as it contributes to the generation of reactive oxygen species (ROS) while increasing photo-oxidative stress in cells. However, precise photo-oxidative response mechanism in non-phototrophic bacteria is yet to be elucidated. In this study, we investigated the effect of BL in Vibrio cholerae by using genetics and transcriptome profiling. Genome-wide analysis revealed that transcription of 6.3% of V. cholerae genes were regulated by BL. We further showed that BL enhances ROS production, which is generated through the oxidative phosphorylation. To understand signaling mechanisms, we generated several knockouts and analyzed their transcriptome under BL exposure. Studies with a double-knockout confirm an anti-sigma factor (ChrR) and putative metalloregulatory-like protein (MerR) are responsible for the genome-wide regulation to BL response in V. cholerae. Collectively, these results demonstrate that MerR-like proteins, in addition to ChrR, are required for V. cholerae to mount an appropriate response against photo-oxidative stress induced by BL. Outside its natural host, V. cholerae can survive for extended periods in natural aquatic environments. Therefore, the regulation of light response for V. cholerae may be a critical cellular process for its survival in these environments. Overall design: mRNA profiles of wild type (WT), ΔChrR, ΔChrRΔMerR and Δcry1Δcry2Δphr mutant V.cholerae cells were generated by deep sequencing, in duplicate, using Illumina MiSeq platform.
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