Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1227990 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Cardiomyocytes with true mitotic potential were enriched by means of CDC20 and SPG20 molecular beacons and analyzed by scRNASeq using the inDrops droplet based encapsulation platform
2019-10-02 | GSE138270 | GEO
Project description:Despite the physiological and pathophysiological significance of microenvironmental gradients, tools for generating such gradients and analysing their impact on cellular phenotypes are lacking. Here we present an integrated microfluidics-based workflow for mimicking extracellular pH gradients characteristic of solid tumors, and studying their multifactorial impact on cancer cells. Our microfluidics device generates a pH gradient across cancer cell 3D cultures in an extracellular matrix. The gradient, validated using pH-sensitive fluorophores can be rapidly controlled to represent spatiotemporal microenvironmental changes, and the device allows high resolution live imaging of, e.g., cell motility and chemotaxis. The device can be reopened, allowing immunofluorescence analysis of phenotypes and spatially resolved analysis of gene expression changes across the pH gradient. The workflow is easily adaptable for other gradients and multiple cell types, making it broadly applicable for integrated analysis of roles of microenvironmental gradients in biology.
2024-05-07 | GSE242233 | GEO
Project description:Loss of Bcl3 influences the abundance and functionality of regulatory T cells in several organs but especially in the intestine. We used single-cell RNA sequencing (scRNAseq) to determine the influence of Bcl3 on cellular basis in a competitive environment.
2024-04-01 | GSE241606 | GEO
Project description:A microfluidics technology was implemented to the immunoaffinity purification process of MHC peptides in Ligandomics/Immunopeptidomics. The thus purified HLA peptides were analysed by LCMS with the nanoElute LC and TimsTOF Pro Mass Spectrometer from Bruker. The aim of the microfluidics implementation was to improve the sensitivity and robustness while also reducing antibody and other material requirements in the immunoaffinity purification protocol.
2022-02-17 | PXD022194 | Pride
Project description:Multinucleated giant hemocytes (MGHs) represent a novel type of blood cell in insects that participate in a highly efficient immune response against parasitoid wasps involving isolation and killing of the parasite. Previously we showed that circulating MGHs have high motility and interaction with the parasitoid rapidly triggers encapsulation, structural and molecular mechanisms behind these processes remained elusive. Here, we use detailed ultrastructural analysis of MGHs and also live cell imaging to study encapsulation in Drosophila ananassae after parasitoid wasp infection. We found dynamic structural changes, mainly driven by the formation of diverse vesicular systems and a large variety of newly developed intracytoplasmic membrane organizations, moreover abundant generation of giant cell exosomes (GCE) in the MGHs. Moreover, we used RNA sequencing to study the transcriptomic profile of MGHs and the activated plasmatocytes 72 hours after infection, as well as the uninduced blood cells. This reveals that differentiation of MGHs is accompanied by broad changes in gene expression. Consistent with the observed structural changes, transcripts mainly related to vesicular function, cytoskeletal organization and adhesion were enriched in MGHs. In addition, transmembrane receptors were upregulated, which may be important for parasitoid recognition. Our results reveal coordinated molecular and structural changes in the course of MGH differentiation and parasitoid encapsulation, providing a mechanistic model for a powerful innate immune response.
2021-12-17 | GSE180960 | GEO
Project description:Global gene expression of Synechocystis sp. PCC 6803 encapsulated in silica gel was examined by microarray analysis. Cultures were encapsulated in gels derived from aqueous precursors and gels derived from alkoxide precursors and incubated under constant light for 24 hours prior to RNA extraction. Cultures suspended in liquid media were also exposed to 500 mM salt stress and incubated under identical conditions, for comparison purposes. The expression of 414 genes was significantly altered by encapsulation in aqueous-derived gels (fold change >/= 1.5 and P-value < 0.01), the expression of 1143 genes were significantly altered by encapsulation in alkoxide derived gels, and only 243 genes were common to both encapsulation chemistries. Additional qRT-PCR analyses of four select genes; ggpS, cpcG2, slr5055, and sll5057, confirmed microarray results. These results illustrate that encapsulation stress is quite different than salt stress in terms of gene expression response. Furthermore, a number of hypothetical and unknown proteins associated with encapsulation and alcohol stress have been identified, with implications for improving encapsulation protocols and rationally engineering microorganisms for direct biofuel production. 16 samples; 4 biological replicates each of 4 treatments
2012-04-23 | E-GEOD-37482 | biostudies-arrayexpress
Project description:The WWOX gene is a tumor suppressor probably involved in variety of cellular processes including and is ferquently downregulated in variety of cancer types. However, its role in endometrial cancerogenesis is not well described. The aim of this study was to characterize how WWOX may be involved in endometrial cancerogenesis, how it influences the basic cancer cell features and modifies cell expression profile.Our observations suggest that in ECC1 endometrial cancer cell line increased expression of WWOX may be involved in the initiation of EMT, leading to changes in cell adhesion and motility but also indicate its suppressive role in the process of mesenchymal phenotype acquisition, resulting in reduction of aggressiveness cell features Well differentiated ECC1 endometrial cancer cells were stably transfected with WWOX cDNA.ECC1 cells transfected with an empty vector served as a control. Total mRNA was isolated to look for gene-expression differences induced by the WWOX overexpression.
2014-09-03 | E-GEOD-61041 | biostudies-arrayexpress
Project description:The WWOX gene is a tumor suppressor probably involved in variety of cellular processes including and is ferquently downregulated in variety of cancer types. However, its role in endometrial cancerogenesis is not well described. The aim of this study was to characterize how WWOX may be involved in endometrial cancerogenesis, how it influences the basic cancer cell features and modifies cell expression profile.Our observations suggest that in ECC1 endometrial cancer cell line increased expression of WWOX may be involved in the initiation of EMT, leading to changes in cell adhesion and motility but also indicate its suppressive role in the process of mesenchymal phenotype acquisition, resulting in reduction of aggressiveness cell features
2014-09-03 | GSE61041 | GEO
Project description:Liver epithelial cells –hepatocytes and bile duct cells– intermingle with a microenvironment of endothelial cells, macrophages and fibroblasts to form the functional unit of the tissue. In homeostasis, the liver epithelium self-renews slowly, yet it is capable of remarkable regeneration following damage. We have shown that liver ductal cells can be expanded in vitro under defined medium to form 3D epithelial 'liver organoids' that recapitulate many aspects of the regeneration process in vitro, yet lack stromal cell components. Here, we describe that a subpopulation of portal mesenchymal cells expressing Sca1 and Pdgfra, exerts a dual effect on the proliferative capacity of ductal cells. On one hand, it supports liver organoid formation and expansion in the absence of exogenous growth factors and independently of cell-to-cell contact. However, when Ductal cells and SCA1+ mesenchymal cells establish physical interaction following a microfluidics encapsulation that enables the cells to self-organize into chimeric organoid structures, cell proliferation is abolished in a mesenchymal-dose dependent manner. We found that it is the ratio between mesenchyme and epithelial cells and not their absolute values that determines the net outcome of ductal proliferation both in vitro, and in vivo, during the different phases of liver regeneration. The mechanism by which Sca1+ mesenchymal cells regulate ductal cell proliferation dynamics is mediated, at least in part, by Notch cell-cell contact inhibition. Our findings underscore how the relative ratio and distribution of cell-cell contacts between the epithelium and its mesenchymal microenvironment are key regulatory processes during the dynamic regulation of tissue regeneration.
2021-11-30 | GSE140697 | GEO
Project description:Cell replacement therapies hold great therapeutic potential. Nevertheless, our knowledge of the mechanisms governing the developmental processes is limited, impeding the quality of differentiation protocols. Generating insulin-expressing cells in vitro is no exception, with the guided series of differentiation events producing heterogeneous cell populations that display mixed pancreatic islet phenotypes and immaturity. The achievement of terminal differentiation ultimately requires the in vivo transplantation of, usually, encapsulated cells. Here we show the impact of cell confinement on the pancreatic islet signature during the guided differentiation of alginate encapsulated human induced pluripotent stem cells (hiPSCs). Our results show that encapsulation improves differentiation by significantly reshaping the proteome landscape of the cells towards an islet-like signature. Pathway analysis is suggestive of integrins transducing the encapsulation effect into intracellular signalling cascades promoting differentiation. These analyses provide a molecular framework for understanding the confinement effects on hiPSCs differentiation while confirming its importance for this process.
2020-01-24 | GSE141891 | GEO