Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Osmolality as a major regulator of the transcriptome and metabolome in kidney collecting duct cells

ABSTRACT: We hypothesized that altered extracellular osmolality per se could affect the transcriptome of the kidney inner medullary collecting duct (IMCD) cells, and hence it might change renal tubular function. The data sets of transcriptomics were incorporated into the "omic" data sets of metabolomics. Primary cultured IMCD cells of rat kidney were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with either reduced (300 mOsm/KgH2O) or the same osmolality for 1 or 2 d more.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE35598 | GEO | 2012/02/09

SECONDARY ACCESSION(S): PRJNA152517

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Osmolality as a major regulator of the transcriptome and metabolome in kidney collecting duct cells

Project description:We hypothesized that altered extracellular osmolality per se could affect the transcriptome of the kidney inner medullary collecting duct (IMCD) cells, and hence it might change renal tubular function. The data sets of transcriptomics were incorporated into the "omic" data sets of metabolomics. Primary cultured IMCD cells of rat kidney were grown in hyperosmolar culture medium (640 mOsm/KgH2O) for 4 d, and then the cells were cultured in the medium with either reduced (300 mOsm/KgH2O) or the same osmolality for 1 or 2 d more. Osmolality stress response. Total RNA from IMCD cells exposed to 300 or 640 mOsm/KgH2O for 24 h (n=3 in each group, 24 h-300 and 24 h-640) or for 48 h (n=3 in each group, 48 h-300 and 48 h-640) after a 4-day-culture in culture media (640 mOsm/KgH2O) were subjected to transcriptome analysis (Affymetrix GeneChip® Rat Gene 1.0 ST array containing 29,215 gene-level probe sets) to profile the gene expression at the mRNA level.

2012-02-09 | E-GEOD-35598 | biostudies-arrayexpress

Vascular calcification is accelerated by hyponatremia and low osmolality condition via activating Rac1-Akt pathway

Project description:Hyponatremia, one of the most frequently observed electrolyte disorders in patients with chronic kidney disease (CKD), is associated with increased mortality. Lower sodium concentrations or low osmolar conditions are shown to induce cell damages via apoptosis and oxidative stress, both of accelerate vascular calcification (VC), a critical phenotype of CKD patients. It is unknown whether hyponatremia or low osmolar condition plays roles in the pathogenesis of VC.Human vascular smooth muscle cells (VSMCs) were cultured with calcifying medium, which was supplemented high calcium and phosphate. Concentrations of sodium in the culture media were further modified to determine the impacts of osmotic pressure on VC. Microarray analysis of VSMCs revealed low osmolality activated Rac1-Akt pathway and reduced expression of NCX1, which is calcium-sodium exchanger.Lower osmolality including hyponatremic condition promotes high-phosphate-induced VC through multiple cellular processes including Rac1-Akt pathway activation.

2023-07-25 | GSE237847 | GEO

Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [single nuclei]

Project description:Single-cell transcriptomics from dissociated organs lack information regarding the spatial origin of each cell, which limits their interpretation, particularly in complex and regionally heterogeneous tissues. This is relevant in the kidney, where cell types are exposed to a wide spectrum of cellular microenvironments along the corticomedullary axis, including steep gradients of extracellular osmolality and oxygen tension. Whether kidney single-cell transcriptomes can be exploited to predict spatial origins of cells and to provide physiological readouts of the cellular microenvironment is unknown. Here, we obtained single-cell transcriptomes of mouse kidney tissue from whole organs and from defined kidney zones (cortex, outer and inner medulla) and applied computational methods to reconstruct the spatial position of kidney tubule cells along the corticomedullary axis based on their transcriptomes. Our approach enabled a spatially resolved analysis of gene expression, showed a coordinated activation of osmolality-and hypoxia-associated genes towards the kidney medulla, and predicted that transcriptomes of a given cell type across different kidney zones change gradually rather than being clearly distinct in different anatomical zones. In genetically modified mice with a tubular concentration defect, spatial reconstruction of single-cell transcriptomics and osmogene expression quantitation accurately predicted reduced medullary osmolality. We conclude that our approach, which can be applied to any mouse whole kidney single-cell transcriptomic dataset, uncovers previously underappreciated information regarding spatial origin and microenvironment-dependent cellular states, adding improved readouts to existing and future datasets.

2020-11-26 | GSE145689 | GEO

Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [Drop-seq]

2020-11-26 | GSE145688 | GEO

MicroRNA (miRNA) expression of IMCD tubule suspension

Project description:miRNA plays a role as post-transcriptional regulator. However, miRNAs in the kidney collecting duct cell have not been well understood. So we aimed to profile miRNAs in the kidney inner medullary collecting duct (IMCD) cells, and to identify the vasopressin-responsive miRNAs in the kidney IMCD cells. The microarray assay revealed that relative expression of miRNAs in the kidney IMCD cells was changed by desmopressin (dDAVP) stimulation. Fresh IMCD tubules were prepared from rat kidney and incubated in the medium in the absence or presence of dDAVP (1 nM, 2 h). Total RNA purified from IMCD tubules was used to analyze miRNA expression by GeneChipM-BM-. miRNA 3.0 Array (Affymetrix).

2014-06-21 | E-GEOD-58693 | biostudies-arrayexpress

Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [bulk RNA-seq]

2020-11-26 | GSE145687 | GEO

MicroRNA (miRNA) expression of IMCD tubule suspension

2014-06-21 | GSE58693 | GEO

Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients

Project description:Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients

| PRJNA607949 | ENA

Transcriptome analysis of pathways and drug transporters after hyperosmotic stress of renal MDCK I cells

Project description:Purpose: To perform pathway analysis of MDCK I treated with hyperosmolality and to investigate how hyperosmolality affects the expression of membrane transporters. Method: MDCK I cells were treated for 24 h with medium supplemented with 200 mOsm raffinose, NaCl or urea (total of 500 mOsm). The control was regular medium (300 mOsm). RNA was isolated from 12 replicates from each condition and a cDNA library was prepared using TruSeq RNA Library Preparation Kit v2 from Illumina following the manufacturer's protocol. The sequencing was done with a HiSeq with single read and a length of 51. The alignment was done with Hisat 2, the count with FeatureCount and the statistical analysis with DESeq2. Results: The pathways the cell cycle, the cytokine-cytokine receptor interaction pathway, and the chemokine-signaling pathway were significantly activated in MDCK I cells after treatment of 200 mOsm raffinose or NaCl (total: 500 mOsm), and not 200 mOsm urea, for 24 hours. Several membrane transporters were regulated by hyperosmolality. Conclusion: Hyperosmolality has an inflammatory-like response in MDCK I cells and it also affects the expression of several membrane transporters.

2018-10-31 | GSE110301 | GEO

Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [single nuclei]

Project description:Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients [single nuclei]

| PRJNA607967 | ENA

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