Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

36 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of E. coli CSH50 wild type and hupA::cm hupB::kan double mutant cells

ABSTRACT: Comparison of transcript profiles of E. coli CSH50 wild-type and CSH50 hupA::cm hupB::kan double mutant cells to distinguish between the genes expressed either in the presence or absence of HU during log phase.

ORGANISM(S): Escherichia coli

SUBMITTER: Georgi Muskhelishvili

PROVIDER: E-MEXP-1742 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of E. coli W3110 wild type and rpoZ mutant cells to distinguish between the genes expressed either in the presence or absence of RNA polymerase omega subunit during log phase

Project description:Comparison of transcript profiles of E. coli W3110 wild-type and rpoZ mutant cells to distinguish between the genes expressed either in the presence or absence of RNA polymerase omega subunit during log phase. Comparison of transcript profiles of E. coli rpoZ mutant cells with or without overproduction of episomal rpoD during the mid log, late log phases and also during transition to stationary phase.

2007-08-01 | E-MEXP-942 | biostudies-arrayexpress

Transcription profiling of E. coli wild type and fis or hns transcription factor mutants in CSH50, LZ41 and LZ54 strains during different growth phases, with relaxation and hypernegative supercoiling and after norflaxacin treatment

Project description:Comparison of transcript profiles of E. coli CSH50 wild-type and fis or hns mutant cells to distinguish between the genes expressed either in the presence or absence of transcriptional regulators FIS and H-NS during different growth phases. Samples were taken in Mid-exponential phase (ME), Transition to Stationary (TS) and Late Stationary phase (LS). <br><br>Effect of FIS and H-NS on gene expression at relaxed and hypernegative supercoiling level was also studied using LZ41 and LZ54 strains. LZ41 and LZ54 strains contain drug-resistant alleles of different topoisomerase genes. In the LZ41 strain norfloxacin treatment strongly relaxes DNA, whereas in the LZ54 strain the same treatment generates high negative supercoiling (Khodursky et al., 1995, PNAS 92:11801-5; Ziechedrich et al, 1997, Genes Dev. 11:2580-92).

2013-01-30 | E-TABM-86 | biostudies-arrayexpress

Roles of relSpn in Stringent Response, Global Regulation, and Virulence of Serotype 2 Streptococcus pneumoniae D39

Project description:Transcriptome analysis of D39 rel+Spn and delta-relSpn strains treated with mupirocin revealed relSpn-independent (translation stress), relSpn-dependent (stringent response), and delta-relSpn-dependent changes suggesting that relSpn and (p)ppGpp amount play wide-ranging homeostatic roles in pneumococcal physiology, besides adjusting macromolecular synthesis and transport in response to nutrient availability. Wildtype and rel deletion mutant (Delta rel) bacteria were grown statically in BHI broth at 37C in an atmosphere of 5% CO2. Cultures were divided in two upon reaching a density of OD620 ~0.1, and lithium mupirocin was added to one culture (t=0) to a final concentration of 100 ng per mL. Treated and untreated cultures were harvested after 20 min further incubation and RNA was extracted by a hot lysis-acid phenol protocol. We performed the following comparisons: Wildtype + mupirocin versus Wildtype untreated (reference); Delta rel + mupirocin versus Delta rel untreated (reference); Delta rel untreated versus Wildtype untreated (reference); Delta rel + mupirocin versus Wildtype + mupirocin (reference). For each comparison, microarray data were obtained from three independent biological replicates and included one dye swap.

2010-05-15 | E-GEOD-14750 | biostudies-arrayexpress

The metalloregulatory site in Streptococcus pneumoniae AdcR, a zinc-activated MarR-family repressor

Project description:Streptococcus pneumoniae D39 AdcR (adhesion competence repressor) is the first metal-sensing member of the MarR (multiple antibiotic resistance repressor) family to be characterized. Expression profiling of a âadcR strain grown in liquid culture under microaerobic conditions revealed that transcript amounts for 13 genes were up-regulated relative to the wild-type strain, among them adcR, adcCBA, encoding a high affinity ABC uptake system for zinc, and genes encoding cell-surface zinc-binding pneumococcal histidine triad (pht) and adcII (lmb, laminin binding) proteins. Down-regulated transcripts included those encoding two putative zinc-containing alcohol dehydrogenases. Bacterial strains were grown exponentially in rich (BHI) media at 37C and an atmosphere of 5% CO2 to OD620~0.2, and were processed as described in the related Sample records. Samples were collected from three independent biological replicates and included one dye swap. Data were normalized using the Lowess (block) method without background subtraction. Changes in relative transcript amounts of positive or negative 2-fold with Bayesian P value of <0.001 were considered significant, and were included as supplementary material for the accompanying manuscript (The metalloregulatory site in Streptococcus pneumoniae AdcR, a zinc-activated MarR-family repressor; Reyes-Caballero, H. et al, manuscript in preparation).

2010-10-01 | E-GEOD-21506 | biostudies-arrayexpress

A new structural paradigm in copper resistance in a human pathogen

Project description:Copper is essential for both innate and adaptive immune function and copper resistance has emerged as an important determinant of virulence of microbial pathogens. In the human pathogen Streptococcus pneumoniae (Spn), cytoplasmic copper resistance is mediated by an operon encoding the copper-responsive repressor CopY, CupA, of unknown function, and CopA, a copper effluxing P1B-type ATPase. We show that CupA is a novel cell membrane-anchored Cu(I) chaperone for CopA, and that a Cu(I)-binding competent, membrane-localized CupA, like CopA, is obligatory for copper resistance. Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2 to a culture density of OD620~0.2 and were processed as described in the related Sample record. Strain IU1781 (D39 rpsL1) served as the reference for the strain comparison. The experiment was repeated one time, and results are consistent with those observed by Shafeeq et al (Mol Microbiol. 2011). Data normalization was performed using the BioArray Software Environment (BASE 1.2; Saal et al, Genome Biol. 2002) using the Lowess (subgrid) method. Median spot intensities were normalized without background subtraction and used to calculate expression ratios. The cut-off for statistical significance of differential expression was set at an average up or down fold change of at least 1.8 fold.

2013-05-24 | E-GEOD-39176 | biostudies-arrayexpress

GM - E. coli - SetB LZ fishns Hyp Rel

Project description:Comparison of transcript profiles of E. coli LZ41 and LZ54 fishns mutant strains containing drug-resistant alleles of different topoisomerase genes to distinguish gene transcripts associated either with relaxation or hypernegative supercoiling in absence of transcriptional regulator FIS and H-NS.

2011-01-07 | E-MEXP-3049 | biostudies-arrayexpress

GM - E. coli - LZ fishns Act Rep

Project description:Comparison of transcript profiles of E. coli LZ41fishns and LZ54fishns strains containing drug-resistant alleles of different topoisomerase genes to distinguish gene transcripts associated either with relaxation or hypernegative supercoiling.

2011-01-07 | E-MEXP-3050 | biostudies-arrayexpress

Transcription profiling of two ancestral and evolved E. coli strains in three evolutionary conditions excess-nutrient adaptation, prolonged stationary phase adaptation and adaptation due to environmental shift

Project description:The mechanism of evolution in different conditions can be examined from various molecular aspects that constitute a cell, namely, transcript, protein or metabolite abundance. We have analyzed transcript and metabolite abundance changes in evolved and ancestor strains in three different evolutionary conditions, namely, excess-nutrient adaptation, prolonged stationary phase adaptation and adaptation due to environmental shift, in two different strains of Escherichia coli K-12 (MG1655 and DH10B).

2007-10-02 | E-MEXP-1166 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis thaliana stems to investigate the transcriptome of myb103 mutants to better understand the mechanism underlying MYB103 action

Project description:Two null mutants of MYB103 were found to have decreased expression of FERULATE-5-HYDROXYLASE and reduced syringyl lignin in the basal inflorescence stem. The aim with this microarray experiment was to investigate the transcriptome of these myb103 mutants to better understand the mechanism underlying MYB103 action.

2012-09-01 | E-MEXP-3680 | biostudies-arrayexpress

Transcription profiling of S. meliloti tolC mutant

Project description:Effect of the deletion of tolC on S. meliloti physiology under free-living conditions

2010-07-01 | E-MEXP-2561 | biostudies-arrayexpress