Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Role of the DNR- and FNR- type regulators in regulation of the denitrification genes in Roseobacter denitrificans OCh114

ABSTRACT: Role of the DNR- and FNR- type regulators in regulation of the denitrification genes in Roseobacter denitrificans OCh114

PROVIDER: PRJNA641392 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Role of the DNR- and FNR- type regulators in regulation of the denitrification genes in Roseobacter denitrificans OCh114

Project description:An aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 has two DNR- and one FNR-type transcriptional regulators, which are predicted to sense nitric oxide and oxygen, respectively. To investigate the role of these regulators in regulation of the denitrification genes, transcriptome profiles of mutant strains of R. denitrificans OCh114 deficient in the genes for the DNR- or FNR-type regulators were determined by NimbleGen Prokaryotic Expression array (12x135K).

2021-06-30 | GSE153074 | GEO

Transcriptome response to oxygen tension and light irradiation in Roseobacter denitrificans OCh114

Project description:Transcriptome profiles of an aerobic photosynthetic bacterium Roseobacter denitrificans OCh114 grown under different oxygen tension and light irradiation conditions were determined by NimbleGen Prokaryotic Expression array (12x135K).

2021-06-30 | GSE152336 | GEO

Roseobacter denitrificans

Project description:Roseobacter denitrificans Genome sequencing

| PRJNA943617 | ENA

Roseobacter denitrificans

Project description:Roseobacter denitrificans Raw sequence reads

| PRJNA937784 | ENA

Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type grown to mid-exponential phase in minimal media with either 13 uM (Cu-H) or 0.5 uM (Cu-L) Cu regimes. The goal was to define the effects of Cu-limitation on denitrification genes Two growth conditions, three biological replicates of each condition. Each sample hybridised in a two-channel hybridization against Paracoccus denitrificans genomic DNA as the comparator/reference, which also acted as a control for spot quality. Cu-concentration 13 uM (Cu-H) versus 0.5 uM Cu (Cu-L) in anaerobic growth conditions.

2013-11-18 | E-GEOD-48577 | biostudies-arrayexpress

Transcriptome analysis of Paracoccus denitrificans during Cu-limitation

2013-11-18 | GSE48577 | GEO

Transcriptome analysis of Paracoccus denitrificans during aerobic and anaerobic respiration (denitrification)

Project description:Transcriptional profiling of Paracoccus denitrificans PD1222 wild type incubated in continuous culture (continuous culture (CSTR)) in minimal media with aerobic or anaerobic conditions. The goal was to define the core respiratory genes.

2017-06-30 | GSE97959 | GEO

Roseobacter denitrificans OCh 114 strain:DSM 7001 | isolate:DSM 7001

Project description:Roseobacter denitrificans DSM 7001 genome sequencing

| PRJNA335203 | ENA

N-terminal-oriented proteogenomics for the marine bacterium Roseobacter denitrificans

Project description:Given the facilities for whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now only based on automated prediction. However, errors in terms of gene structure are still frequently reported especially for the correct determination of initiation start codons. Here, we propose a strategy to enrich and detect protein N-termini by mass spectrometry in order to refine genome annotation. After selective protein N-termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPPAc-OSu) as labeling reagent, protein digestion was performed with three proteases in parallel. TMPP-labeled N-terminal-most peptides were further resolved from internal peptides by the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting methodology before analysis with tandem mass spectrometry. We refined the annotation of the genome of a model marine bacterium, Roseobacter denitrificans.

2014-02-19 | PXD000337 | Pride

Transcriptome sequencing of Paracoccus denitrificans ATCC19367 with florfenicol exporsure

Project description:We report the application of transcriptome sequencing technology in florfenicol interfering with denitrification by Paracoccus denitrificans. More than 30 billion bases of sequences were obtained by sequencing analysis. We found 433 differentially expressed genes, of which 292 genes were down-regulated and 141 genes were up-regulated, respectively. Importantly, most of the denitrification genes were suppressed, which further led to the enrichment of key metabolic pathways. The weakening of protein synthesis was consistent with the bacteriostatic mechanism of florfenicol. In particular, we found 42 putative differentially expressed sRNAs. After homologous alignment, target gene prediction and functional analysis, it was proved that the sRNAs differential expression profile is likely to be a key transcription factor affected by antibiotics in denitrification. This study provides new ideas for further control of environmental antibiotic pollution.

2021-04-13 | GSE166910 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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