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Transcriptomic response to calcium in normal colon organoids is impacted by colon location and sex

ABSTRACT: Here, we used bulk RNA-seq data derived from healthy colon organoids exposed to two differing calcium concentrations. Through the use of external single cell RNA-seq data, we estimate changes in cell composition and gene expression brought about by high calcium conditions and relate those effects to colorectal cancer.

ORGANISM(S): Homo sapiens

PROVIDER: GSE196168 | GEO | 2022/10/12

REPOSITORIES: GEO

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Ethanol exposure drives colon location-specific cell composition changes in a normal colon crypt 3D organoid model

Project description:Here, we used bulk RNA-seq data derived from healthy colon organoids (un)exposed to ethanol. Through the use of external single cell RNA-seq data, we estimate changes in cell composition that are more pronounced in distal colon organoids following ethanol treatment. We extend this analysis by inferring cell-type-specific effects of ethanol treatment on colon organoids.

2020-12-14 | GSE150027 | GEO

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

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

Project description: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.

2021-12-14 | GSE166464 | GEO

Calcium is a global regulator in Vibrio parahaemolyticus

Project description:Here we probe the global response to calcium in the marine bacterium and pathogen Vibrio parahaemolyticus by using transcriptome, reporter and phenotypic analyses. Swarming gene expression and motility were enhanced by calcium. Calcium also stimulated expression and function of one of the organismM-bM-^@M-^Ys two type three secretion systems (T3SS1 but not the T3SS2). Although low calcium is an inducing signal for the T3SS of many organisms, calcium stimulation of T3SS has not been reported before. EGTA was also a stimulus for T3SS1 expression and activity; however this appeared to be the consequence of iron rather than calcium chelation. LafK, a key regulator of swarming genes, was found necessary for calcium induction of T3SS1 gene transcription and cytotoxicity. Regulation of swarming and T3SS1 were additionally linked by a negative feedback loop propagated by ExsA. Overexpression of exsA was used to probe the extent of the T3SS1 regulon and verify its coincident induction by calcium and EGTA. The calcium transcriptome analysis revealed a calcium-repressed LysR-type transcriptional regulator; CalR was shown to repress swarming and T3SS1 gene expression. Thus in V. parahaemolyticus, calcium influences gene expression and behavior and seems a signal pertinent for surface colonization and virulence. The gene expression profiles of Vibrio parahaemolyticus cells grown on rich medium or medium supplemented with CaCl2 or EGTA were compared using Affymetrix custom microarrays.

2010-11-05 | E-GEOD-22190 | biostudies-arrayexpress

Calcium is a global regulator in Vibrio parahaemolyticus

Project description:Here we probe the global response to calcium in the marine bacterium and pathogen Vibrio parahaemolyticus by using transcriptome, reporter and phenotypic analyses. Swarming gene expression and motility were enhanced by calcium. Calcium also stimulated expression and function of one of the organism’s two type three secretion systems (T3SS1 but not the T3SS2). Although low calcium is an inducing signal for the T3SS of many organisms, calcium stimulation of T3SS has not been reported before. EGTA was also a stimulus for T3SS1 expression and activity; however this appeared to be the consequence of iron rather than calcium chelation. LafK, a key regulator of swarming genes, was found necessary for calcium induction of T3SS1 gene transcription and cytotoxicity. Regulation of swarming and T3SS1 were additionally linked by a negative feedback loop propagated by ExsA. Overexpression of exsA was used to probe the extent of the T3SS1 regulon and verify its coincident induction by calcium and EGTA. The calcium transcriptome analysis revealed a calcium-repressed LysR-type transcriptional regulator; CalR was shown to repress swarming and T3SS1 gene expression. Thus in V. parahaemolyticus, calcium influences gene expression and behavior and seems a signal pertinent for surface colonization and virulence.

2010-11-05 | GSE22190 | GEO

serum exosomes contain SPARC and LRG1 as biomarkers for colon cancer and differ by tumor primary location

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2019-11-25 | PXD012283 | Pride

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2020-12-31 | E-MTAB-5687 | biostudies-arrayexpress

Calcium-Restricted Lipid Remodeling Drives Ferroptosis Resistance

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2018-01-25 | GSE109611 | GEO

Cytosolic calcium and nuclear calcium-regulated transcription networks in response to ABA and JA

Project description:Cytosolic calcium and nuclear calcium-regulated transcription networks in response to ABA and JA

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