Project description:Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in stationary phase (10 h). Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in stationary phase (10 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of phoU1 or phoU2. Results: The expression of 2 genes were significantly decreased and no genes was significantly increased in expression level due to the loss of phoU1 expression.The expression of 279 genes were significantly decreased and 716 genes were significantly increased in expression level due to the loss of phoU2 expression.
Project description:Transcriptome Comparison of staphylococcus aureus phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (12 h)
Project description:MGAS315 is a wild type strain. RNA isolated in exponential phase and stationary phase were compared Keywords: Growth phase comparison
Project description:Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in log-phase (6 h) Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in log-phase (6 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of phoU1 or phoU2 in log-phase (6 h). Results: The expression of 23 genes were significantly decreased and 69 genes was significantly increased in expression level due to the loss of phoU1 expression.The expression of 474 genes were significantly decreased and 471 genes were significantly increased in expression level due to the loss of phoU2 expression.
Project description:Proteomic analysis of Staphylococcus aureus strain NCTC8325 (MRSA) grown in rich medium. This strain produces 97% of persister in stationary phase. Exponential and stationary phase MRSA were compared to elucidate pathways that are modulated in the persister state compared to dividing cells.
Project description:We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent. To this end, gene expression data for a histone knock-out (?ura3?hpyA) strain versus parent (?ura3) were collected. The histone deletion mutant and parent strain, at log and stationary phase, were compared to the common reference strain NRC-1 (log). There are three biological replicates each, plus dye-flips, for a total of 24 arrays
Project description:Objective of the study is to find out the differentially regulated genes of Mycobacterium BCG strain in extended stationary phase comparison to log phase growth and resuscitation phase. Mycobacterium BCG culture was grown in Sauton medium at 37o C without shaking. Cells at A600 0.6-0.8 were harvested as log phase culture. The cells harvested after 5 months incubation at 37oC without shaking became non culturable and were harvested as extended stationary phase cells. The extended stationary phase cells were treated with resuscitation promoting factor (Rpf) from Micrococcus luteus and harvested after 8 days. Cells of this stage were treated as resuscitation phase cells. Gene expression profiling was carried out using Agilent microarray platform. Keywords: Extended stationary phase, Log phase growth and Resuscitation phase.
Project description:Transcriptome analysis of two independently derived hns mutants compared to an isogenic wild-type Salmonella (strain 14028s - lab ID# WN153). Note: both the wild-type and hns strains carry an additional mutation in the rpoS locus (encoding the stationary phase sigma factor) resulting in a deletion of amino acids 61-65 that diminish its activity. Keywords: cell type comparison
Project description:The custom-made S. epidermidis GeneChips(Shanghai Biochip Co., Ltd) included qualifiers representing open reading frame (ORF) sequences identified in the genomes of the S. epidermidis strain RP62A, as well as unique ORFs in S. epidermidis strain 12228. The GeneChips were composed of cDNA array containing PCR products of 2316 genes and oligonucleotide array containing 252 genes.Two-component regulatory systems (TCSs) play a pivotal role in bacterial adaptation, survival, and virulence by sensing changes in the external environment and modulating gene expression in response to a variety of stimuli.To investigate the regulatory role of LytSR, one of the TCSs identified in the genomes of S. epidermidis, we used the GeneChips to perform a transcriptional profile analysis of the wild strain and lytSR mutant.
