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Staphylococcus epidermidis

ABSTRACT: Transcriptome Comparison of phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (10 h)

PROVIDER: PRJNA382568 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5443790_1.fastq.gz	Fastqsanger.gz
	SRR5443790_2.fastq.gz	Fastqsanger.gz
	SRR5443782_1.fastq.gz	Fastqsanger.gz
	SRR5443782_2.fastq.gz	Fastqsanger.gz
	SRR5443783_1.fastq.gz	Fastqsanger.gz

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Staphylococcus epidermidis

Project description:Transcriptome Comparison of phoU Homologies Genes Deletion strain and the Parent Strain in log-phase (6 h).

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Transcriptome Comparison of staphylococcus aureus phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (12 h)

Project description:Transcriptome Comparison of staphylococcus aureus phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (12 h)

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Transcriptome Comparison of phoU Homologies: Genes Deletion strain and the Parent Strain in stationary phase (10 h)

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.

2017-10-03 | GSE97656 | GEO

GAS M3 serotype, exponential versus stationary phase

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Histone dosage and gene expression changes in Halobacterium salinarum

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

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Expression analysis of hns mutant Salmonella

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

2006-06-08 | GSE4931 | GEO

Phage SEP1 hijacks S. epidermidis stationary cells metabolism to replicate

Project description:In nature, bacteria often survive in a stationary state, with low metabolic activity. Phages use the metabolic machinery of the host cell to replicate and, therefore, their efficacy against non-dividing cells is usually limited. Nevertheless, it was previously shown that the Staphylococcus epidermidis phage SEP1 has the remarkable capacity to actively replicate in stationary-phase cells, reducing their numbers. Here, we studied for the first time the transcriptomic profiles of both exponential and stationary cells infected with SEP1 phage, using RNA-seq, to have a better understanding of this rare phenomenon. We showed that SEP1 successfully takes over the transcriptional apparatus of both exponential and stationary cells. Infection was, however, delayed in stationary cells, with genes within the gp142-gp154 module putatively implicated in host takeover. S. epidermidis responded to SEP1 infection by upregulating three genes involved in a DNA modification system, with this being observed already 5 min after infection in exponential cells and later in stationary cells. In stationary cells, a significant number of genes involved in translation and RNA metabolic and biosynthetic processes were upregulated after 15 and 30 min of SEP1 infection in comparison with the uninfected control, showing that SEP1 activates metabolic and biosynthetic pathways necessary to its successful replication.

2024-05-15 | GSE254200 | GEO

Transcription profiling of E.coli WT3100 and phoU mutant

Project description:Comparison of gene experission profiles of Ecoli WT3110 and phoU mutant Experiment Overall Design: DNA microarray analysis of the PhoU mutant with the wild type strain W3110 as a control. The PhoU mutant and the wild type strain were grown in MOPS minimal medium overnight when the RNA was isolated using MasterPure RNA Purification Kit and reverse transcribed for making probes for array hybridization on Affymetrix microarrays.

2008-06-15 | E-GEOD-7243 | biostudies-arrayexpress

Transcriptome Comparison of phoU Homologies Genes Deletion strain and the Parent Strain in log-phase (6 h).

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.

2017-10-03 | GSE97400 | GEO

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