Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Oxygen exposure increases resistance of Desulfovibrio vulgaris Hildenborough to hydrogen peroxide inactivation

ABSTRACT: Differences in gene expression between a mutant D. vulgaris strain missing the PerR transcriptional regulator gene and the wild-type strain. For each condition (PerR_cDNA_vrs_gDNA, wild-type_cDNA_vrs_gDNA) 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference. Log2 PerR mutant versus wild-type gene expresson with growth on WP-lactate. SUPPLEMENTARY FILES: * Log2 gene expression ratios of PerR mutant/wild-type (PerR/gDNA/ wildtype/gDNA) and q-values. * Wild type raw data. * PerR mutant raw data.

ORGANISM(S): Desulfovibrio vulgaris str. Hildenborough

SUBMITTER: Sean Caffrey

PROVIDER: E-GEOD-26448 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Function of Periplasmic Hydrogenases in the Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

Project description:The sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough possesses four periplasmic hydrogenases to facilitate the oxidation of molecular hydrogen. These include an [Fe], a [NiFeSe] and two [NiFe] hydrogenases encoded by the hyd, hys, hyn1 and hyn2 genes, respectively. In order to understand their cellular functions the expression levels of these hydrogenases, along with the growth rate analysis of mutant strains, was determined during growth on defined media under 3 different conditions. These conditions incuded lactate or hydrogen at either 5% or 50% (vol/vol) used as the sole electron donor for sulfate reduction. Keywords: Electron donor change For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference. After total intensity normalization the SAM (significance analysis of microarrays) was used to find differentially expressed genes.

2010-06-10 | E-GEOD-8137 | biostudies-arrayexpress

Gene expression of D. vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions

Project description:The gene expression profile of wild-type Desulfovibrio vulgaris grown on cathodic hydrogen, generated at an iron electrode surface with an imposed negative potential of -1.1 V (cathodic protection conditions). The gene expression profile of cells grown on cathodic hydrogen was compared to that of cells grown with gaseous hydrogen bubbling through the culture. Relative to the latter, the electrode-grown cells over-expressed two hydrogenases, the hyn1 genes for [NiFe] hydrogenase-1, and the hyd genes, encoding [Fe] hydrogenase. The hmc genes for the high molecular weight cytochrome (Hmc) complex, which allows electron flow from the hydrogenases across the cytoplasmic membrane, were also over-expressed. In contrast, cells grown on gaseous hydrogen over-expressed the hys genes for [NiFeSe] hydrogenase. Cells growing on the electrode also over-expressed genes encoding proteins which promote biofilm formation. Although the gene expression profiles for these two modes of growth were distinct, they were more closely related to each other than to that for cells grown in a lactate- and sulfate-containing medium. Electrochemically measured corrosion rates were lower for iron electrodes covered with hyn1-, hyd-, and hmc-mutant biofilms, as compared to wild-type biofilms. This confirms the importance, suggested by the gene expression studies, of the corresponding gene products in D. vulgaris-mediated iron corrosion. Keywords: Growth on Iron Electrode and Biofilm formation For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

2010-05-26 | E-GEOD-10388 | biostudies-arrayexpress

Effect of sulfide on growth physiology and gene expression of Desulfovibrio vulgaris Hildenborough

Project description:The effect of sulfide stress on Desulfovibrio vulgaris Hildenborough (DvH) gene expression was determined by comparing the gene expression profiles of DvH under conditions in which sulfide was allowed to accumulate (high sulfide, average concentration 10 mM) against DvH cells grown under conditions in which sulfide was removed by continuous gassing (low sulfide, average concentration 1 mM). High sulfide significantly decreased the instantaneous growth rate constant and final cell density of the culture indicating a decreased bioenergetic fitness. Changes in gene expression caused by exposure to high sulfide were determined using full-genome DvH microarrays. The transcription of ribosomal protein-encoding genes was decreased, in agreement with the lower growth rate of DvH under high sulfide conditions. Interestingly, expression of the gene for DsrD, located downstream of the genes for dissimilatory sulfite reductase (DsrAB) was also strongly down-regulated. In contrast, the expression of many genes involved in iron accumulation, stress response and proteolysis, and chemotaxis were increased. This indicates that high sulfide represents a significant stress condition, in which the bioavailability of metals like iron may be lowered and in which proteins (e.g. metalloenzymes) may need to be refolded, or proteolytically degraded. Overall this leads to a reduced growth rate and less efficient biomass production with available resources. For each condition 2 unique biological samples were hybridized to 4 arrays that each contained duplicate spots. Genomic DNA was used as universal reference.

2010-05-06 | E-GEOD-15073 | biostudies-arrayexpress

S. coelicolor YSK3225 R5- Medium Time-course Study (Culture #1)

Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarray methods to investigate the temporal transcriptome profiles of S. coelicolor A3(2) âabsA1::apr mutant strain and compared with the M145 Wild-type strain (series submitted separately). Keywords: Time course Time-course study involved analysis of 12 samples (11h, 19h, 22h, 24h, 26h, 28h, 31h, 32h, 35h, 37h, 38h and 41h). All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.

2010-06-11 | E-GEOD-8108 | biostudies-arrayexpress

S. coelicolor YSK3225 R5- Medium Time-course Study (Culture #2)

Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarray methods to investigate the temporal transcriptome profiles of S. coelicolor A3(2) âabsA1::apr mutant strain and compared with the M145 Wild-type strain (series submitted separately). Keywords: Time course Time-course study involved analysis of 6 samples (18h, 24h, 26h, 28h, 32h and 42h). All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.

2010-06-10 | E-GEOD-8109 | biostudies-arrayexpress

S. coelicolor YSK4425 R5- Medium Time-course Study (Culture #1)

Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarray methods to investigate the temporal transcriptome profiles of S. coelicolor A3(2) âafsS::apr mutant strain and compared with the M145 Wild-type strain (series submitted separately). Keywords: Time course Time-course study involved analysis of 8 samples (16h, 20h, 22h, 24h, 26h, 31h, 37h and 40h). All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.

2010-06-10 | E-GEOD-8110 | biostudies-arrayexpress

Legionella pneumophila transcriptomic response of hfq mutant during post-exponential phase

Project description:Legionella pneumophila wild-type and hfq mutant were grown to post-exponential. The wild-type strain is used as the control. Two strains: wild-type (control) and hfq mutant (test). Three biological replicates. Ch1 is gDNA, use as a reference channel (Talaat, 2002, NAR)

2013-05-21 | E-GEOD-42905 | biostudies-arrayexpress

Array competitive genomic hybridization of three Saccharomyces cerevisiae strains vs. DBY8268

Project description:A six array study using total gDNA recovered from two separate cultures of each of three different strains of Saccharomyces cerevisiae (YB-210 or CRB, Y389 or MUSH, and Y2209 or LEP) and two separate cultures of Saccharomyces cerevisiae DBY8268. Each array measures the hybridization of probes tiled across the Saccharomyces cerevisiae genome. Biological replicates: 2 for each strain, 2 for control. Grown and harvested in parallel. One replicate per array.

2014-10-01 | E-GEOD-56441 | biostudies-arrayexpress

Transcription profiling of Pseudomonas putida strains with wild type and inactivated vacB alleles

Project description:Transcriptome comparison of two isogenic strains, one with a wild type vacB allele and another with an inactivated vacB allele

2008-09-01 | E-MEXP-1440 | biostudies-arrayexpress

Transcription profiling of Pseudomonas putida strains with wild type and inactivated cyoB alleles

Project description:Transcriptome comparison of two isogenic strains, one with a wild type cyoB allele and another with an inactivated cyoB allele

2022-11-21 | E-MEXP-639 | biostudies-arrayexpress

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