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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SncRNAs in E. faecalis V538

ABSTRACT: Small non coding RNA molecules (sncRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sncRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. Enterococcus faecalis. We characterized 11 sncRNAs by tiling microarray analysis, 5’ and 3’ RACE-PCR, and Northern blot analysis. Six sncRNAs were specifically expressed at exponential phase, two sncRNAs were observed at stationary phase, and three were detected during both phases. This is the first experimental genome-wide identification of sncRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen. Identification of sncRNA candidates transcribed by E. faecalis V583 was undertaken with two samples of cells harvested in mid-log growth phase and stationary phase after 24h of incubation at 37°C in M17 glucose media.

ORGANISM(S): Enterococcus faecalis V583

SUBMITTER: jean-christophe giard

PROVIDER: E-GEOD-28741 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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sncRNAs in E. faecalis V538

Project description:Small non coding RNA molecules (sncRNAs) are key mediators of virulence and stress inducible gene expressions in some pathogens. In this work we identify sncRNAs in the Gram positive opportunistic pathogen Enterococcus faecalis. Enterococcus faecalis. We characterized 11 sncRNAs by tiling microarray analysis, 5’ and 3’ RACE-PCR, and Northern blot analysis. Six sncRNAs were specifically expressed at exponential phase, two sncRNAs were observed at stationary phase, and three were detected during both phases. This is the first experimental genome-wide identification of sncRNAs in E. faecalis and provides impetus to the understanding of gene regulation in this important human pathogen.

2011-04-21 | GSE28741 | GEO

Transcriptomic response of Enterococcus faecalis to iron excess

Project description:To further investigate the homeostatic response of E. faecalis to Fe exposure, we examine the whole-genome transcriptional response of wild-type (WT) exposed to non toxic Fe excess. This experiment correspond the work titled Transcriptomic response of Enterococcus faecalis to iron excess (work in preparation) A four chip study using total RNA recovered from four separate wild-type cultures of Enterococcus faecalis OG1RF, two controls samples (N medium growth) and two iron samples (N medium gowth with 0.5 mM Fe-NTA). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).

2012-03-01 | E-GEOD-34432 | biostudies-arrayexpress

Transcription profiling by array of Enterococcus faecalis V19 wild type and SlyA mutant cells

Project description:SlyA (EF_3002) mutant of Enterococcus faecalis V19 was constructed.Three samples of wild type and mutant cells were grown in M17 media at 37°C and harvested in mid-exponential growth phase. RNA were extracted and used for global transcriptomic analysis.

2010-09-30 | E-MEXP-2903 | biostudies-arrayexpress

Transcriptome analysis of Enterococcus faecalis OG1 delta-EF2638 mutant

Project description:Analysis of changes in gene expression in Enterococcus faecalis OG1 delta-EF2638 mutant compared to wild-type OG1 strain. The deletion mutant has a growth defect when grown with aeration The mutant presented in this study is described and characterized in Vesic, D. and Kristich, C.J. 2012. A Rex-family transcriptional repressor influnces H2O2 accumulation by Enterococcus faecalis. (submitted for publication) Microarray analysis was done using RNA isolated from two independent cultures of wild-type Enterococcus faecalis OG1 and two independent cultres of Enterococcus faecalis OG1 delta-EF2638 mutant; each RNA sample was subjected to triplicate hybridization (technical replicates) . Microarrays were custom designed to investigate expression of ORFs in Enterococcus faecalis OG1RF genome. The arrays were designed based on the OG1RF annotation generated with the Rapid Annotation Using Subsystem Technology (RAST) server (Aziz et. al. 2008. BMC Genomics 9:75), as described in Frank et al (2012) Infect. Immun. 80:539. The aim was eighteen probe pairs per ORF, each of which is present in triplicate.

2013-04-15 | E-GEOD-43228 | biostudies-arrayexpress

The SOS response controls intrinsic resistance to cephalosporins

Project description:Comparison of the transcription profile between Enterococcus faecalis V583 strain and its mutant having a constitutive SOS response

2017-07-05 | E-MEXP-3861 | biostudies-arrayexpress

Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels

Project description:The microarrays experiments was performed with the purpose of identify transcriptional networks activated by copper. This experiment correspond the work tituled Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels (work in preparation).Mauricio Latorrea,b, Jessica Galloway-PeM-CM-1ac,d,e, Jung Hyeo Rhoc,d, Marko Budinichf, Barbara E. Murrayc,d,e, Alejandro Maassb,f, Mauricio GonzM-CM-!leza,b,f*. a INTA, Laboratorio de BioinformM-CM-!tica y ExpresiM-CM-3n GM-CM-)nica, INTA, Universidad de Chile, Santiago, Chile. b Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile. c Division of Infectious Disease, Department of Medicine, University of Texas Medical School, Houston, Texas, United States of America. d Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School, Houston, Texas, United States of America. e Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America f Mathomics, Center for Mathematical Modeling (UMI2807CNRS), Santiago, Chile. * Corresponding author. Address: El LM-CM--bano 5524, Santiago 11, Chile. Fax: +56 (2) 2214030. A eight chip study (two technical replicates) using total RNA recovered from four separate cultures of: Enterococcus faecalis OG1RF (N medium growth), Enterococcus faecalis OG1RF copM-NM-^T mutant strain (N medium growth), Enterococcus faecalis OG1RF copM-NM-^T mutant low copper treatment (N medium growth + 0.05 mM CuSO4) and Enterococcus faecalis OG1RF copM-NM-^T mutant low copper treatment (N medium growth + 0.5 mM CuSO4). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).

2013-11-12 | E-GEOD-45131 | biostudies-arrayexpress

Transcriptional profiling of wild type vs rex-deficient mutants of Enterococcus faecalis V583

Project description:The transcriptional profiles of wild type Enterococcus faecalis V583 and two rex-deficient mutants (EF2638 and EF2933) were compared

2013-03-07 | E-MTAB-1219 | biostudies-arrayexpress

RNA-seq of phage VPE25 treated Enterococcus faecalis OG1RF relative to untreated controls

Project description:Temporal transcriptomic response of Enterococcus faecalis OG1RF during phage VPE25 infection

2019-12-05 | E-MTAB-8546 | biostudies-arrayexpress

Transcription profiling of Enterococcus faecalis wild type, delta-relA and delta-relAsp (partial deletion) strains

Project description:Two mutants of the relA gene of Enterococcus faecalis were constructed, one (delta-relA) carrying a whole deletion of the gene, the other (delta-relAsp) carrying a partial deletion of its 3' extremity. the 3 strains were cultured to mid exponential growth phase in M17 medium, and RNAs were extracted using the RNeasy Midi Kit (QIAGEN). <br>RNAs were subjected to 2 DNase treatments, and prepared for chips hybridization.

2009-12-29 | E-MEXP-2112 | biostudies-arrayexpress

Transcription profiling time series of Enterococcus faecalis V583 in response to growth in 10% and 100% blood

Project description:Gene expression of Enterococcus faecalis V583 in response to growth in 10% and 100% blood was examined by the use of of genome wide microarrays. Transcriptional profiles were obtained through time series experiments over periods of 60min (for 10% blood) and only after 30 min for growth 100% blood.

2009-10-13 | E-TABM-541 | biostudies-arrayexpress

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