Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homeostatic calcium fluxes, ER calcium release, SOCE, and calcium oscillations in cultured astrocytes are interlinked by a small calcium toolkit

ABSTRACT: We report the application of RNA-seq for molecular profiling of cultured, cortical astrocytes. Our data set is based on about 40 million unique reads per sample in four independent mRNA preparations. Cortical astrocytes are a prototypical cell model for investigating calcium signaling. For analysis of calcium fluxes, we performed direct calcium imaging in the endoplasmic reticulum and in the cytosol. We describe in our study the physiological profile of homeostatic and agonist-induced calcium fluxes. Furthermore, we show how ER calcium release shapes the cytosolic calcium signal. This transcriptome dataset was used to profile the calcium toolkit of astrocytes. The data suggest that a small number of calcium signaling-related proteins mediate calcium homeostasis in astrocytes.

ORGANISM(S): Mus musculus

PROVIDER: GSE166464 | GEO | 2021/12/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Homeostatic calcium fluxes, ER calcium release, SOCE, and calcium oscillations in cultured astrocytes are interlinked by a small calcium toolkit

Project description:Homeostatic calcium fluxes, ER calcium release, SOCE, and calcium oscillations in cultured astrocytes are interlinked by a small calcium toolkit

| PRJNA701007 | ENA

Homeostatic SOCE prevents complex cell stress responses

Project description:We report the application of bulk RNA-seq for detection of changes in the mRNA-transcriptome of cultured primary, cortical astrocytes when homeostatic calcium fluxes are modulated. We investigated three conditions: (1) control (2) glial cells treated with thapsigargin, a blocker of the SERCA. This causes the depletion of ER calcium and induces store-operated calcium entry (SOCE). (3) Calcium-free extracellular solution. This causes an acute interruption of homeostatic calcium influx and thereby also causes ER calcium depletion. The aim was to detect immediate changes in the cellular transcriptome. Therefore, we treated the cells for just 60 min with the different conditions. The data show that about 8% (calcium-free condition) or 16% (SERCA blockade) of the whole mRNA transcriptome is changed within one hour, when homeostatic calcium fluxes are affected. Regulated are biological processes associated with cell health, differentiation, metabolism, ER stress responses, gene expression, and many more processes.

2024-07-09 | GSE242678 | GEO

Calcium Toolkit genes expression in the zebrafish brain

Project description:Calcium Toolkit genes expression in the zebrafish brain

| PRJNA525447 | ENA

Calcium Toolkit genes expression in the zebrafish brain

Project description:Zebrafish are well suited for in vivo calcium imaging because the transparency of their larvae and the ability to express calcium probes in various cell subtypes. This model organism has been used extensively to study brain development, neuronal function, and network activity. However, only a few studies have investigated calcium homeostasis and signaling in zebrafish neurons, and little is known about the proteins that are involved in these processes. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. Based on quantitative real-time polymerase chain reaction arrays, we estimated the relative mRNA levels in the brain of CaTK genes at two developmental stages. In both 5 dpf larvae and adult zebrafish, the highest relative expression was observed for tmbim4, which encodes a Golgi membrane protein. The present data on CaTK genes will contribute to future applications of zebrafish as a model for in vivo and in vitro studies of Ca2+ signaling.

2019-03-05 | GSE127335 | GEO

Control of calcium oscillations by membrane fluxes.

Project description:It is known that Ca(2+) influx plays an important role in the modulation of inositol trisphosphate-generated Ca(2+) oscillations, but controversy over the mechanisms underlying these effects exists. In addition, the effects of blocking membrane transport or reducing Ca(2+) entry vary from one cell type to another; in some cell types oscillations persist in the absence of Ca(2+) entry (although their frequency is affected), whereas in other cell types oscillations depend on Ca(2+) entry. We present theoretical and experimental evidence that membrane transport can control oscillations by controlling the total amount of Ca(2+) in the cell (the Ca(2+) load). Our model predicts that the cell can be balanced at a point where small changes in the Ca(2+) load can move the cell into or out of oscillatory regions, resulting in the appearance or disappearance of oscillations. Our theoretical predictions are verified by experimental results from HEK293 cells. We predict that the role of Ca(2+) influx during an oscillation is to replenish the Ca(2+) load of the cell. Despite this prediction, even during the peak of an oscillation the cell or the endoplasmic reticulum may not be measurably depleted of Ca(2+).

| S-EPMC337063 | biostudies-literature

Control of glycolytic enzyme fluxes in Saccharomyces cerevisiae

Project description:Metabolic fluxes may be regulated "hierarchically," e.g., by changes of gene expression that adjust enzyme capacities (V(max)) and/or "metabolically" by interactions of enzymes with substrates, products, or allosteric effectors. In the present study, a method is developed to dissect the hierarchical regulation into contributions by transcription, translation, protein degradation, and posttranslational modification. The method was applied to the regulation of fluxes through individual glycolytic enzymes when the yeast Saccharomyces cerevisiae was confronted with the absence of oxygen and the presence of benzoic acid depleting its ATP. Metabolic regulation largely contributed to the approximately 10-fold change in flux through the glycolytic enzymes. This contribution varied from 50 to 80%, depending on the glycolytic step and the cultivation condition tested. Within the 50-20% hierarchical regulation of fluxes, transcription played a minor role, whereas regulation of protein synthesis or degradation was the most important. These also contributed to 75-100% of the regulation of protein levels. Keywords: Condition comparison

2007-10-17 | GSE9232 | GEO

Ethanol exposure reveals persistent and categorizable astrocyte calcium response types and associated gene signatures

Project description:Various EtOH doses increased intracellular calcium in a subset of astrocytes, identifying three cellular response types categorized by response waveform properties S- (sustained), T- (transient), or M- (Mixed), along with non-responsive (NR) astrocytes. By single-cell RNA-seq analysis of astrocytes from the different response types, we report type-enriched discriminatory gene expression signatures and provide a basis for identifying the relationship between susceptibility to EtOH effects in the astrocyte subgroups and corresponding measurable markers of calcium signal and gene expression.

2022-07-27 | GSE199025 | GEO

hictk: blazing fast toolkit to work with .hic and .cool files

Project description:We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.

2023-09-14 | GSE242815 | GEO

Calcium bursts allow rapid reorganization of EFhD2/Swip-1 crosslinked actin networks in epithelial wound closure

Project description:Changes in cell morphology require the dynamic remodeling of the actin cytoskeleton. Calcium fluxes have been suggested as an important signal to rapidly relay information to the actin cytoskeleton, but the underlying mechanisms remain poorly understood. Here, we identify the EF-hand domain containing protein EFhD2/Swip-1 as a conserved lamellipodial protein strongly upregulated in Drosophila macrophages at the onset of metamorphosis when macrophage behavior shifts from quiescent to migratory state. Loss- and gain-of-function analysis confirm a critical function of EFhD2/Swip-1 in lamellipodial cell migration in fly and mouse melanoma cells. Contrary to previous assumptions, TIRF-analyses unambiguously demonstrate that EFhD2/Swip-1 proteins efficiently cross-link actin filaments in a calcium-dependent manner. Using a single-cell wounding model, we show that EFhD2/Swip-1 promotes wound closure in a calcium-dependent manner. Mechanistically, our data suggest that transient calcium bursts reduce EFhD2/Swip-1 cross-linking activity and thereby promote rapid reorganization of existing actin networks to drive epithelial wound closure.

2022-04-19 | GSE200966 | GEO

Transcription profiling of S. cerevisiae treated with absence of oxygen or depletion of ATP to investigate control of glycolytic enzyme fluxes

2008-06-16 | E-GEOD-9232 | biostudies-arrayexpress