Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tracking the elusive function of Bacillus subtilis Hfq (Agilent)

ABSTRACT: Transcriptomic analysis of Bacillus subtilis wild-type strain and hfq mutant in stationary phase of growth using to tiling array gene expression analysis. RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. 97 transcription units (representing 134 genes) were found significantly different between the wild-type and the ΔhfqBs strains in the stationary cultures performed in rich LB medium.

ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168

PROVIDER: GSE66892 | GEO | 2015/06/22

SECONDARY ACCESSION(S): PRJNA278272

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Tracking the elusive function of Bacillus subtilis Hfq (Agilent)

Project description:Transcriptomic analysis of Bacillus subtilis wild-type strain and hfq mutant in stationary phase of growth using to tiling array gene expression analysis. RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. 97 transcription units (representing 134 genes) were found significantly different between the wild-type and the ?hfqBs strains in the stationary cultures performed in rich LB medium. This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ?hfq mutant were examined 5 h after the onset of stationary phase in LB medium. Two biological replicates were analyzed.

2015-06-22 | E-GEOD-66892 | biostudies-arrayexpress

Tracking the elusive function of Bacillus subtilis Hfq (NimbleGen)

Project description:Transcriptomic analysis of Bacillus subtilis hfq mutant in exponential phase of growth. Wild-type strain and hfq mutant cells in exponentially growth phase were subjected to tiling array gene expression analysis. RNA-binding protein Hfq is a key component of the adaptive responses of many proteobacterial species. In these organisms, the importance of Hfq largely stems from its participation to regulatory mechanisms involving small non-coding RNAs. In contrast, the function of Hfq in Gram-positive bacteria has remained elusive. Hfq does not appear to influence B.subtilis RNA patterns during the exponential phase to any significant extent, at least in cells grown in rich medium. This data set contains 4 samples. Expression profiles of Bacillus subtilis prototype strain (BSB1, a tryptophan-prototrophic derivative 168 strain) and a ?hfq mutant were examined at OD ~0.5 in LB medium. Two biological replicates were analyzed.

2015-06-22 | E-GEOD-66891 | biostudies-arrayexpress

Tracking the elusive function of Bacillus subtilis Hfq (NimbleGen)

2015-06-22 | GSE66891 | GEO

Transcriptional profiles of Salmonella typhimurium wt, hfq and smpB mutants in four different growth conditions

2008-12-13 | GSE11486 | GEO

Transcriptional profiles of Salmonella typhimurium wt, hfq and smpB mutants in four different growth conditions

Project description:S. typhimurium 14028 wt, hfq and smpB were harvested from log phase LB (LBlog); (2), stationary phase LB (LBstat); (3) 4h MgM medium pH 5.0 after resuspension of LB stat culture (MgMshock); and (4) log phase MgM medium pH5.0 after 100fold dilution of an LB stat culture (MgMDil). Total RNA was extracted, cDNA labeled and hybridized to a non-redundant Salmonella whole genome PCR product ORF array. S. typhimurium 14028 cells were harvested, on three separate days, (1), after growth at 30°C to log phase in LB (LBlog); (2), after growth at 30°C to stationary phase in LB (LBstat); (3) after transfer of a stationary phase culture grown in LB into magnesium-deficient MgM medium [100 mM Tris-Cl, 5 mM KCl, 7.5 mM (NH4)2SO4, 0.5 mM K2SO4, 1 mM KH2PO4, 0.2% glycerol, 0.1% Casamino acids, 8uM MgCl2] pH 5.0 and growth for four more hours at 30°C (MgMshock); (4) after 100fold dilution of a stationary phase culture grown in LB into magnesium-deficient MgM medium pH5.0 and growth at 30°C to log phase (MgMDil). This procedure was performed on (A), wild type [WT] cells; (B), cells of an hfq- (STM4361) knockout mutant; and (C), cells of an smpB- (STM2688) knockout mutant, resulting in 36 samples total. Total RNA was extracted, cDNA labeled with Cy5-dCTP and hybridized versus Cy3-labeled 14028 gDNA to a non-redundant Salmonella whole genome PCR product ORF array.

2008-12-12 | E-GEOD-11486 | biostudies-arrayexpress

Tracking the elusive function of Bacillus subtilis Hfq

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-06-22 | GSE66893 | GEO

Tracking the Elusive Function of Bacillus subtilis Hfq.

Project description: Not available

| S-EPMC4410918 | biostudies-literature

Tracking the elusive function of Bacillus subtilis Hfq

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-06-22 | E-GEOD-66893 | biostudies-arrayexpress

Hfq virulence regulation in enterohemorhagic Escherichia coli O157:H7 strain 86-24

Project description:Escherichia coli O157:H7 is a food-borne pathogen that causes bloody diarrhea and hemolytic uremic syndrome. Hfq is an sRNA chaperone protein that is involved in post-transcriptional regulation of virulence genes in pathogenic bacteria. In EHEC strain EDL933, Hfq acts a negative regulator of the locus of enterocyte effacement (LEE) that encodes most of the proteins involved in type three secretion and attaching and effacing lesions. We deleted hfq in E. coli O157:H7 strain 86-24 and compared global transcription profiles of the hfq mutant to the wild type strain in exponential growth phase. Deletion of hfq affected transcription of genes common to nonpathogenic and pathogenic strains of E. coli as well as pathogen-specific genes. Downregulated genes in the hfq mutant included ler as well as genes encoded in LEE2-5 that encode for type three secretion and AE lesion formation. Decreased expression of the LEE genes in the hfq mutant occurred at mid-, late, and stationary growth phases in both LB and DMEM media as detected by qRT-PCR. We also confirmed decreased regulation of the LEE genes by examining secreted proteins and AE lesion formation by the hfq mutant and WT strains. Deletion of hfq also caused decreased expression of the two-component system qseBC involved in inter-kingdom signaling and virulence gene regulation in EHEC as well as an increase in stx2AB expression that encodes for the deadly Shiga toxin. Altogether, these data indicate that Hfq plays a different regulatory role in EHEC 86-24 from what has been reported for EHEC strain EDL933 and that the role of Hfq in EHEC virulence regulation extends beyond the LEE.

2012-01-06 | GSE30893 | GEO

Identification of Hfq bound RNA by co-immunoprecipitation and RNA-sequencing

Project description:Co-immunoprecipitation with endogenous Hfq3xFlag in exponential, stationary, non-induced and virulence induced conditions, followed by RNA-sequencing, revealed 1697 mRNAs and 208 ncRNAs associated with Hfq. We identified 56 new ncRNAs and validated 3 Hfq-dependent trans sRNAs on by Northern blot analysis. Interestingly, 55% of the ncRNAs were encoded antisense to a protein coding sequence. Abundance of 4 asRNAs and their corresponding target mRNAs was altered upon hfq, indicating a substantial influence of Hfq on asRNA-target interactions.

2014-12-04 | GSE59123 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data