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ProteomicsSmall Extracellular Vesicles derived from four dimensional-culture of mesenchymal stem cells induce alternatively activated macrophages by upregulating IGFBP2/EGFR to attenuate inflammation in the spinal cord injury of rats
Effectively reducing the inflammatory response after spinal cord injury (SCI) is a challenging clinical problem and the subject of active investigation. This study employed a porous scaffold-based three dimensional long-term culture technique to obtain human umbilical cord mesenchymal stem cell (hUC...
ORGANISM(S): Homo sapiens (Human) 
2023-07-20 | PXD040516 | Pride
Spinal cord injury  small extracellular vesicles  four dimensional culture  macrophage polarization  igfbp2/egfr 
TranscriptomicsExpression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture
3D cultivation of cells lead to changes in morphology of the cells. This is likely to explain the higher radioresistance of cells growing in 3D compared to cells growing in 2D cell culture. Whole genome gene expression is performed to determine genes involved in changes of cell moroholgy and radiore...
ORGANISM(S): Homo sapiens 
2010-07-30 | E-GEOD-17347 | biostudies-arrayexpress
TranscriptomicsThree-dimensional low shear culture of Mycobacterium bovis BCG induces biofilm formation and antimicrobial drug tolerance
Mycobacteria naturally grow as corded biofilms in liquid media without detergent. Such detergent-free biofilm phenotypes may reflect the growth pattern of bacilli in tuberculous lung lesions. New strategies are required to treat tuberculosis that is responsible for more deaths each year than any oth...
ORGANISM(S): Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2 
2021-01-29 | E-MTAB-9904 | biostudies-arrayexpress
TranscriptomicsGene expression analysis of MCF7 breast cancer cells cultured as xenografts, in two dimensional cultures, in polyHEMA anchorage independent three dimansional cell culture models and in Matrigel three dimensional cultures.
The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-...
ORGANISM(S): Homo sapiens 
2013-10-30 | E-GEOD-47583 | biostudies-arrayexpress
MetabolomicsMass Spectrometry Imaging of Lipids in a Gut Epithelial Cell Model

Scope: The Caco2/HT29-MTX co-culture system is widely used as a cell model of the intestinal epithelium. Although the gut epithelium plays an important role in the uptake of free fatty acids and the resynthesis of triglycerides, the lipid distribution profile of the two-dimensional co-culture sys...

2025-06-14 | MTBLS12599 | MetaboLights
TranscriptomicsCharacterization of a tetra-culture system combining lung alveolar epithelial cells, endothelial cells, macrophages, and mast cells in a three-dimensional orientation
To more accurately model inhalation toxicity in vitro, we developed a tetra-culture system that combines lung alveolar epithelial cells, endothelial cells, macrophages, and mast cells in a three-dimensional orientation. We characterized the influence of the added complexity, using network perturbati...
ORGANISM(S): Homo sapiens 
2019-02-12 | E-MTAB-7072 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of control and MMP-14 (MT1-MMP) expressing MCF-7 cells growing in three-dimensional (3D) type I collagen gels versus monolayer cell culture conditions
In order to investigate the impact of MMP-14 (MT1-MMP) and three-dimensional (3D) culture conditions on the transcriptomes of a human breast adenocarcinoma cell line, we performed a microarray analysis from RNAs isolated from MCF-7 cells expressing either an empty vector (CTRL) or human MMP-14 cDNA ...
ORGANISM(S): Homo sapiens 
2014-12-15 | E-GEOD-49595 | biostudies-arrayexpress
ProteomicsMESENCHYMAL STROMAL CELLS FROM THREE-DIMENSIONAL CULTURE MITIGATE IV VITRO EXTRACELLULAR TRAPS INDUCED BY LIPOPOLYSACCHARIDES
Neutrophil extracellular traps (NETs) are characterized as extracellular DNA fibers comprised of histone and granular proteins. NETs play a crucial role in defense against systemic infections, inflammation, autoimmune disorders and cancer. However, excessive NETs release can increase inflammatory pr...
ORGANISM(S): Mus musculus (Mouse) 
2026-08-15 | PXD067214 | Pride
Mesenchymal stromal cells Neutrophil extracellular traps 3d culture 
TranscriptomicsTranscription profiling by array to investigate effect of repeated cigarette exposure on three-dimensional human bronchial epithelial cultures
Cigarette smoke (CS) is a major risk factor in the development of chronic inflammatory lung diseases such as chronic obstructive pulmonary disease. To evaluate the biological impact of CS on lung tissue, three-dimensional (3D) organotypic bronchial tissue cultures can be used to replicate in vivo co...
ORGANISM(S): Homo sapiens 
2018-09-30 | E-MTAB-6175 | biostudies-arrayexpress
TranscriptomicsHigh-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells.
The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-...
ORGANISM(S): Homo sapiens 
2013-10-30 | E-GEOD-42529 | biostudies-arrayexpress
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