Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

How cyanobacteria pose new problems to old methods: Challenges in microarray time series analysis

ABSTRACT: Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells

ORGANISM(S): Synechocystis sp. PCC 6803

PROVIDER: GSE45667 | GEO | 2013/04/02

SECONDARY ACCESSION(S): PRJNA195575

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

How cyanobacteria pose new problems to old methods: Challenges in microarray time series analysis

Project description:Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells We quantified circadian gene expression of the wild type Synechocystis PCC6083 strain. Over a 24 h time course, 6 samples for RNA isolation were taken at the following time points: 30 minutes before and after light is switched off (sample 1 - CT 11.5 and sample 2 - CT 12.5), 30 minutes before midnight (sample 3 - CT 17.5), 348 30 minutes before and after light onset (sample 4 - CT 23.5 and sample 5 - CT 0.5) and 30 minutes before noon (sample 6 - CT 5.5).

2013-04-02 | E-GEOD-45667 | biostudies-arrayexpress

Lysine methylation in cyanobacteria

Project description:Deciphering structure, function and mechanism of a new lysine methyltransferase cKMT1 in model cyanobacterium Synechocystis sp. PCC 6803

2022-07-29 | PXD035617 |

Group 2 Sigma Factors Are Central Regulators of Oxidative Stress Acclimation in Cyanobacteria

Project description:The model cyanobacterium Synechocystis sp. PCC encodes nine different σ factors. SigA is the essential primary σ factor that is mainly responsible for expression of housekeeping genes during normal growth. Group 2 σ factors are non-essential in standard conditions, and actually all single, double, triple and quadruple inactivation strains of group 2 factors grow well in standard growth conditions. The roles of group 2 σ factors in oxidative stress acclimation were studied using the ΔsigBCDE strain of Synechocystis sp. PCC 6803 which is devoid of all group 2 σ factors, and triple inactivation strains, each containing one group 2 σ factor. The ΔsigBCD strain contains only SigE, ΔsigBCE only SigD, ΔsigBDE only SigC and ΔsigCDE only SigB. The expression of genes encoding known players of oxidative stress tolerance in the triple and quadruple mutants were compared in standard growth conditions using DNA microarray analysis.

2018-11-12 | GSE117478 | GEO

Exploring the extracellular landscape of cyanobacteria with deep exoproteomics

Project description:Extracellular proteins are involved in a remarkable number of fundamental processes in cyanobacteria. Yet, there is limited knowledge regarding the identity and function of these proteins. Here, we introduce a solid-phase enhanced protein aggregation workflow that enables description of the cyanobacterial exoproteome with unprecedented depth. Application to cyanobacteria from three distinct habitats, Synechocystis sp. PCC 6803, Synechcoccus sp. PCC 11901 and Nostoc punctiforme PCC 73102, allowed the identification of up to 62% of all predicted secreted proteins. The approach was then extended to compare the Synechocystis sp. PCC 6803 wild-type secretome with that of a bloom-like aggregated state and a secretion-impaired mutant. Finally, we demonstrate that the workflow can be miniaturized and adapted to a 96-well format for high-throughput secretome analysis. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and point to a functional conservation of the secretome across species from different environments. Our approach can be applied to microbes from a wide range of habitats, with the potential to open new avenues of investigation in microbial exoproteomics.

2024-08-29 | PXD047856 | Pride

Self-assembly of nanofilaments in cyanobacteria for protein co-localization

Project description:Shotgun proteomics of Synechocystis sp. PCC 6803 and Synechococcus elongatus UTEX 2973 expressing PduA*

2023-10-14 | MSV000093111 | MassIVE

Synechocystis sp. PCC 6803 trophic condition

Project description:Targeted proteome analysis of Synechocystis sp. PCC 6803 under photoautotrophic and mixotrophic conditions

2020-06-02 | PXD010010 | JPOST Repository

Sll0171 regulates the trimethylation of sll1694 affecting phototactic motility in Cyanobacteria

Project description:Sll0171 affects the phototaxis of Synechocystis sp. PCC 6803 by regulating the level of trimethylation at K168 of sll1694.

2024-12-10 | PXD058756 |

The role of the Synechocystis sp. PCC 6803 homolog of the circadian clock output regulator RpaA in day-night transitions

Project description:Like many other organisms, cyanobacteria exhibit rhythmic gene expression with a period length of 24 hours to adapt to daily environmental changes. In the model organism Synechococcus elongatus PCC 7942 the central oscillator consists of three proteins: KaiA, KaiB and KaiC and utilizes the histidine kinase SasA and its response regulator RpaA as output-signaling pathway. Synechocystis sp. PCC 6803 contains two additional homologs of the kaiB and kaiC genes. Here we demonstrate that RpaA interacts with the core oscillator KaiAB1C1 of Synechocystis sp. PCC 6803 via SasA, similar to Synechococcus elongatus PCC 7942. However, interaction with the additional Kai homologs was not detected, suggesting different signal transduction components for the clock homologs. Inactivation of rpaA in Synechocystis sp. PCC 6803, lead to reduced viability of the mutant in light-dark cycles that aggravated under mixotrophic growth conditions. Chemoheterotrophic growth in the dark was abolished completely. In accordance, transcriptomic data revealed that RpaA is involved in the regulation of genes related to CO2‑acclimation and carbon metabolism under diurnal light conditions. Further, our results indicate that RpaA functions in the posttranslational regulation of glycogen metabolism as well, and a potential link between the circadian clock and motility was identified.

2018-10-01 | GSE116795 | GEO

Examination of gene expression levels in mutants of phytochrome-related protain

Project description:To identify novel phototransduction pathways in cyanobacteria, mutants defective for phytochrome-related proteins in Synechocystis sp. PCC 6803 that exhibit increased or decreased gene expression levels. were screened. Keywords: array-based

2007-01-01 | GSE5391 | GEO

Active site of cyanobacterial RNA polymerase compensates for the absence of proofreading factors [Synechoscystis sp]

Project description:We found that cyanobacterial RNA polymerase possesses very efficient intrinsic proofreading ability. This ability allows model species of cyanobacteria, Synechocystis sp PCC 6803 to keep in vivo level of transcriptional mistakes close to that of E.coli.

2018-08-15 | GSE115134 | 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