Transcriptome profiling of madin-darby canine kidney cells with canine parvovirus 2a persistent infection
Ontology highlight
ABSTRACT:
ORGANISM(S): Canis lupus familiaris Canis lupus
PROVIDER: GSE72397 | GEO | 2016/12/01
SECONDARY ACCESSION(S): PRJNA293948
REPOSITORIES: GEO
Similar Datasets
Project description:cDNA expression array of epithelial phenotype untreated MDCK cells; after 30 days of TGFb treatment, which induces a mesenchymal phenotype; TGF-b-treated cells that are treated with 5-AZA for 72 h; and 30 days after TGFb withdrawal Gene expression was analyzed in a genome-wide manner, to asses those changes occurring upon TGF-b-induced epithelial to mesenchymal transition (EMT), those that are stimulated by treatment with a demethylating agent, and which are restored after TGF-b withdrawal
2014-08-14 | GSE48525 | GEO
Project description:Madin-Darby Canine Kidney (MDCK) cells are widely used to study epithelial cell functionality. Their low endogenous drug transporter protein levels make them an amenable system to investigate trans-epithelial permeation and drug transporter protein activity after their transfection. MDCK cells display diverse phenotypic traits and as such laboratory-to-laboratory variability in drug permeability assessments are observed. Consequently, In Vitro-In Vivo extrapolation (IVIVE) approaches using permeability and/or transporter activity data require calibration. A comprehensive proteomic quantification of eleven filter-grown parental or mock-transfected MDCK monolayers from eight different pharmaceutical laboratories using the Total Protein Approach (TPA) is provided. TPA enabled estimations of key morphometric parameters such as monolayer cellularity and volume. Overall, metabolic liability to xenobiotics is likely to be limited for MDCK cell due to the low expression of required enzymes. SLC16A1 (MCT1) was the highest abundance SLC transporter linked to xenobiotic activity, while ABCC4 (MRP4) was the highest abundant ABC transporter. Our data supports existing findings that Claudin-2 levels may be linked to tight junction modulation, thus impacting trans-epithelial resistance. This unique database provides data on more than 8000 proteins copy number and concentrations, thus allowing an in-depth appraisal of the control monolayers used in each laboratory.
2023-07-20 | PXD039552 | Pride
Project description:The paracellular passage of ions in epithelial systems is dictated by the repertoire of tight junction (TJ) proteins, the number and architecture of apicolateral TJ strands, and the interaction of TJ proteins with the cytoskeleton. To investigate the relative contribution of these factors and to explore their regulation, we examined a passage number dependent phenotypic change in Madin Darby Canine Kidney (MDCK) cells iteratively passaged at low density in which dilution potentials of the monolayer abruptly decreased but transepithelial resistance (TER) progressively increased. Here, we report that the phenotypic transition involved a decrease surface expression of peanut agglutinin (PNA), a decrease in steady state levels of claudin-1 and a slight decrease in E-cadherin expression in the context of an apparently claudin-2-negative system. Late passage cells grew in more densely packed monolayers and exhibited characteristics of a competent, functional cultured monolayer including inducible vectorial ion transport in response to norepinephrine (NE) and sphere formation in three dimensional laminin gel culture. Microarray analysis of gene expression levels in early and late passage cells revealed an increase in transcript abundance for SGK and GLUT-3, and a reduction Id-3. The steady state protein expression levels of GLUT-3, however, were found to be equivalent. These findings suggest that the expression of claudin-2 in MDCK cells could be contingent on signaling via lateral cell contacts and that claudin-1, in the context of sustained claudin-8 expression, could function as a negative regulator of overall TER.
2010-02-13 | GSE14837 | GEO
Project description:cDNA expression array of epithelial phenotype untreated MDCK cells; after 30 days of TGFb treatment, which induces a mesenchymal phenotype; TGF-b-treated cells that are treated with 5-AZA for 72 h; and 30 days after TGFb withdrawal Gene expression was analyzed in a genome-wide manner, to asses those changes occurring upon TGF-b-induced epithelial to mesenchymal transition (EMT), those that are stimulated by treatment with a demethylating agent, and which are restored after TGF-b withdrawal Two replicates for untreated and TGFb treated, and one sample for 5-AZA and TGFb withdrawal
2014-08-14 | E-GEOD-48525 | biostudies-arrayexpress
Project description:The paracellular passage of ions in epithelial systems is dictated by the repertoire of tight junction (TJ) proteins, the number and architecture of apicolateral TJ strands, and the interaction of TJ proteins with the cytoskeleton. To investigate the relative contribution of these factors and to explore their regulation, we examined a passage number dependent phenotypic change in Madin Darby Canine Kidney (MDCK) cells iteratively passaged at low density in which dilution potentials of the monolayer abruptly decreased but transepithelial resistance (TER) progressively increased. Here, we report that the phenotypic transition involved a decrease surface expression of peanut agglutinin (PNA), a decrease in steady state levels of claudin-1 and a slight decrease in E-cadherin expression in the context of an apparently claudin-2-negative system. Late passage cells grew in more densely packed monolayers and exhibited characteristics of a competent, functional cultured monolayer including inducible vectorial ion transport in response to norepinephrine (NE) and sphere formation in three dimensional laminin gel culture. Microarray analysis of gene expression levels in early and late passage cells revealed an increase in transcript abundance for SGK and GLUT-3, and a reduction Id-3. The steady state protein expression levels of GLUT-3, however, were found to be equivalent. These findings suggest that the expression of claudin-2 in MDCK cells could be contingent on signaling via lateral cell contacts and that claudin-1, in the context of sustained claudin-8 expression, could function as a negative regulator of overall TER. 3 biological replicates of early and late passage were run on Affymetrix chips. the replicates were averaged then compared.
2010-04-09 | E-GEOD-14837 | biostudies-arrayexpress
Project description:To gain more information about EMT induced by oncogenic Ras in MDCK cells, we performed RNA-seq of MDCK and MDCK-Ras cells and compared their genome-wide gene expression profiles.
2016-02-03 | E-MTAB-3301 | biostudies-arrayexpress
Project description:Purpose: When we infect MDCK epithelial cells we low dosage of Listeria monocytogenes we observe that at late times (24 h) post infection that infected cells pertaining in infection foci get collectively extruded out of the epithelial monolayer forming a 3D mound. The formation of the infection mound results from the competition between two populations: the uninfected cells ("surrounders") that eventually squeeze and extrude the infected cells ("mounders"). Using RNA-Sequencing, we performed gene expression profiling for uninfected MDCK cells, cells infected for 24 h with Listeria monocytogenes at an MOI of 200 (both "mounders" and "surrounders") and cells sorted to infected ("mounders") or uninfected ("surrounders") populations after being infected for 24 h with Listeria monocytogenes. Our goal was to understand how transcriptional regulation leads to the collective extrusion of infected epithelial cells triggered by surrounding uninfected cells. Methods and Results: By analyzing the differentially expressed genes between all conditions we find a significant number of up- or down-regulated genes between all groups. Through pathway enrichemnet analysis we find that compared to cells not exposed to infection "mounders" showed significant downregulation in 31 genes related to tight junctions and ZO-1 was one of the key genes downregulated and to a lesser degree to pathways related to adherens junctions, focal adhesions and regulation of the actin cytoskeleton. "Surrounders" showed significant downregulation to genes related to actin cytoskeleton, to endocytosis to ahderens junctions and to a lesser degree focal adhesions and tight junctions. Especially "surrounders" and to a lesser degree "mounders" showed upregulation on IL-17 and NF-kB and TNF related signaling pathways, which underlines the fact that although "surrounders" are uninfected their distinct mechanical behavior might arise from cytokines released from "mounders" which impact crucially their phenotype. Interestingly "mounders" only showed additionally upregulation on DNA replication, cell cycle related pathways and ferroptosis suggesting that these cells might be undergoing some kind of stress response. Conclusions: Infection of MDCK epithelial cells with Listeria monocytogenes significantly alters the transcriptome of the infected host cells when those are examined 24 h post infection. Both infected and uninfected cells in an infected well show significant transcriptomic changes compared to uninfected cells but also compared to each other. Most importnantly innate immunity related pathways are singificanlty upregulated for un infected cells in an infected well and to a lesser degree for infected cells as compared to cells not exposed to infection.
2019-11-19 | GSE140626 | GEO
Project description:In order to gain insight into epithelial morphogenesis and the influence of culture geometry on gene expression patterns, Madin Darby Canine Kidney (MDCK) epithelial cells where grown in 2-dimensional (2D) culture or 3-dimensional (3D) culture . MDCK cells cultured in 2D were plated atop a pre-solidified type I collagen gel. Cells cultured under these conditions grew as flat monolayer sheets. In 3D culture, cells are embedded within type I collagen gel. Cells grown under these conditions form large spherical cysts with hollow central lumens. We anticipate, therefore, that these results provide insight into the mechanisms that regulate epithelial cystogenesis.
2013-06-03 | GSE28381 | GEO
Project description:To gain more information on the expression of microRNAs during EMT induced by oncogenic Ras in MDCK cells, we performed deep sequencing (Illumina HiSeq2000) of MDCK and MDCK-Ras cells and compared their genome-wide microRNA expression profiles. RNA-Seq data from the same study has also been deposited at ArrayExpress under accession number E-MTAB-3301 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3301/).
2015-11-17 | E-MTAB-3302 | biostudies-arrayexpress
Project description:In order to gain insight into epithelial morphogenesis and the influence of culture geometry on gene expression patterns, Madin Darby Canine Kidney (MDCK) epithelial cells where grown in 2-dimensional (2D) culture or 3-dimensional (3D) culture . MDCK cells cultured in 2D were plated atop a pre-solidified type I collagen gel. Cells cultured under these conditions grew as flat monolayer sheets. In 3D culture, cells are embedded within type I collagen gel. Cells grown under these conditions form large spherical cysts with hollow central lumens. We anticipate, therefore, that these results provide insight into the mechanisms that regulate epithelial cystogenesis. Cells grown in the 2D or 3D geometries were collected from digested type I collagen gels on day 8. The 2D MDCK cells were treated as the control condition and there gene expression patterns were compared to those of 3D grown cells, which served as the experimental condition.
2013-06-03 | E-GEOD-28381 | biostudies-arrayexpress