Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (microarobic conditions)

ABSTRACT: Transcriptional profiling of R. sphaeroides Δlov comparing to control R. sphaeroides 2.4.1 under microarobic conditions Two strain experiment under microarobic conditions. 6 Biological replicas, independetly grown and harvested at OD660=0,8 - 1-3 pooled in replicate 1 and 4-6 pooled in replicate 2

ORGANISM(S): Rhodobacter sphaeroides 2.4.1

SUBMITTER: Sebastian Metz

PROVIDER: E-GEOD-33194 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

R. sphaeroides delta-CryB vs. R. sphaeroides 2.4.1 microarobic conditions

Project description:Transcriptional profiling of R. sphaeroides delta-CryB comparing to control R. sphaeroides 2.4.1 under microaerobic conditions Two strain experiment under microaerobic conditions. 9 Biological replicas, independetly grown and harvested at OD660=0,8; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2, 7-9 pooled in replicate 3

2011-11-09 | E-GEOD-33554 | biostudies-arrayexpress

R. sphaeroides delta-cryB

Project description:This SuperSeries is composed of the following subset Series: GSE33553: R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 photo-oxidative stress, aerobic conditions GSE33554: R. sphaeroides delta-CryB vs. R. sphaeroides 2.4.1 microarobic conditions GSE33555: R. sphaeroides delta-cryB vs. R. sphaeroides 2.4.1 under blue light, semiaerobic conditions Refer to individual Series

2011-11-09 | E-GEOD-33556 | biostudies-arrayexpress

Role of a short LOV protein in blue light- and singlet oxygen-dependent gene regulation in Rhodobacter sphaeroides

Project description:The facultatively photosynthetic bacterium Rhodobacter sphaeroides harbors an unusual LOV (light, oxygen, voltage) domain protein, RsLOV. While showing a characteristic photocycle, the protein misses a C - terminal output domain, similar to PpSB2 in Pseudomonas putida. Oxygen tension and light quantity are the two main responsible factors controlling the expression of photosynthesis genes in Rhodobacter sphaeroides. Two photoreceptor proteins are known to be involved in this regulation: the intensively studied AppA protein and the more recently identified cryptochrome-like protein CryB. Here we show by transcriptome and physiological studies that RsLOV is also involved in the regulation of photosynthetic gene expression. Our data further hint to a connection between RsLOV and the carbon hydrate metabolism, chemotaxis, as well as to the cellular response to photooxidative stress. RsLOV does not only affect blue light dependent gene expression but also redox-dependent regulation. This SuperSeries is composed of the following subset Series: GSE33194: R. sphaeroides ?lov vs. R. sphaeroides 2.4.1 (microarobic conditions) GSE33259: R. sphaeroides ?lov vs. R. sphaeroides 2.4.1 (blue light, semiaerobic conditions) GSE33260: R. sphaeroides ?lov vs. R. sphaeroides 2.4.1 (singlet oxygen stress, aerobic conditions)

2011-10-25 | E-GEOD-33261 | biostudies-arrayexpress

Rhodobacter sphaeroides WT 2.4.1 under singlet oxygen stress

Project description:Transcriptional and translational profiling of R. sphaeroides WT 2.4.1 under singlet oxygen stress compared to control (no stress) conditions RNA samples collected at time-point zero and at different time-points after singlet oxygen stress were analyzed by two-color microarrays

2012-11-14 | E-GEOD-42244 | biostudies-arrayexpress

R. sphaeroides Δlov vs. R. sphaeroides 2.4.1 (singlet oxygen stress, aerobic conditions)

Project description:Transcriptional profiling of R. sphaeroides Δlov compared to control R. sphaeroides 2.4.1 under singlet oxygen stress, aerobic conditions Two-strain experiment with overnight cultures of the wild type 2.4.1 and the Δlov mutant. Both were diluted to an OD660 of 0.2 and gassed to adjust aerobic conditions (≈ 170 µM O2). 0.2 µM of methylene blue was added to the cultures to act as photosensitizer. After one doubling time of growth in the darkness cells were illuminated with 800 W m-2 of white light for 7 min.

2011-10-25 | E-GEOD-33260 | biostudies-arrayexpress

Rhodobacter sphaeroides 2.4.1 adaptation to high concentrations of Cobalt ions

Project description:To further characterize the capability of R. sphaeroides to cope with high cobalt ion concentrations, we combined the selection of adaptive defective mutants, carried out by negative selection of transposon insertional libraries on 5 mM Co2+ enriched solid medium, with the analysis of growing capacities and transcriptome profiling of a selected mutant (R95).

2014-03-07 | E-MTAB-2284 | biostudies-arrayexpress

Rhodobacter sphaeroides 2.4.1 pSurS versus pBBR under singlet oxygen stress.

Project description:To learn more about the function of SurS, we constructed an over-expression strain. For this purpose, the surS gene together with its native RpoE promoter was cloned into the middle-copy plasmid pBBR1 and expressed in the R. sphaeroides wild-type 2.4.1 background. The corresponding strain consequently exhibits a singlet oxygen-induced SurS over-expression compared to an empty vector control. Total RNA from the over-expression (pSurS) and from the empty vector control (pBBR) strain was extracted after 7 min of singlet oxygen stress and used for microarray analysis to investigate SurS-induced changes on transcriptome level. RNA samples collected after 7 min of singlet oxygen stress were analyzed by two-color microarrays. Each microarray contains a pool of three independent biological replicates for each sample.

2014-07-04 | E-GEOD-59046 | biostudies-arrayexpress

IscR of Rhodobacter sphaeroides functions as repressor of genes for iron-sulphur metabolism and represents a new type of iron-sulphur binding protein

Project description:Iron-sulphur (Fe-S) clusters are ensembles of iron and sulphide centres. They are found in all life forms and are important components of many enzymes involved in diverse cellular processes, including respiration, DNA synthesis or gene regulation. However, the increase in oxygen after the emergence of oxygenic photosynthesis created a threat to FeM-bM-^@M-^SS proteins and, consequently, to the organisms relying on them. Therefore, bacteria have evolved mechanisms to maintain a precise intracellular iron concentration. A major role of IscR in R. sphaeroides iron dependent regulation was suggested in a bioinformatic study , which predicted a binding site in the upstream regions of several iron uptake genes. Most known IscR proteins have Fe-S clusters featuring (Cys)3(His)1 ligation. However, IscR proteins from Rhodobacteraceae harbour only one Cys residue and it was considered unlikely that they can ligate an Fe-S cluster. In this study, the role of R. sphaeroides IscR as transcriptional regulator and sensor of the Fe-S cluster status of the cell was analysed. The results provide evidence that R. sphaeroides IscR functions as transcriptional repressor of genes involved in iron metabolism by binding to the predicted DNA binding motif. Furthermore, IscR possesses a unique Fe-S cluster ligation scheme with only a single cysteine involved. RNA samples collected from a control strain (wild type 2.4.1) and of the iscR deletion strain (2.4.1M-bM-^HM-^FiscR) were analyzed by two-color microarrays

2015-02-03 | E-GEOD-65537 | biostudies-arrayexpress

R. sphaeroides pRPcrZ vs. R. sphaeroides pR4352 under low oxygen conditions

Project description:Transcriptional profiling of R. sphaeroides pRPcrZ compared to control R. sphaeroides pR4352 under low oxygen conditions. In this study we compared the transcriptome of a PcrZ over-expression strain to a control strain. PcrZ is the first small non-coding RNA, which is involved in the complex regulatory network of photosynthesis gene regulation in Rhodobacter sphaeroides. It counteracts the formation of photosynthetic complexes in a redox dependent manner. Two-strain experiment at low oxygen conditions (0.5 mg/L O2)

2012-08-14 | E-GEOD-37381 | biostudies-arrayexpress

R. sphaeroides Δirr vs. R. sphaeroides 2.4.1 under microaerobic conditions

Project description:Transcriptional profiling of R. sphaeroides Δirr compared to control R. sphaeroides 2.4.1 under microaerobic conditions. Two strain experiment under microarobic conditions (30 µM). 6 Biological replicas, independetly grown and harvested at OD660=0,4; 1-3 pooled in replicate 1, 4-6 pooled in replicate 2

2011-11-09 | E-GEOD-33534 | 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