Expression data for 3D versus 2D cell culture
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1183397 | ENA |
REPOSITORIES: ENA
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Project description:We examined whether SATB1 functions as a global gene regulator in order to maintain the aggressive phenotype of the MDA-MB-231 cell line. We compared the gene expression profiles between control_shRNA-MDA-MB-231 cells, which express SATB1 at high levels, and SATB1_shRNA1-MDA-MB-231 in which the level of SATB1 was greatly downregulated by RNAi technology. This comparative studies were performed using two different platforms (Codelink and Affymetrix genechip) with two culture conditions either on plastic dish (2D) or on matrigel (3D) which allows cells to form a breast-like morphology only for non-aggressive cells. Keywords: Comparative studies on Control_shRNA and SATB1_shRNA1 expressing MDA-MB-231 from 2D or 3D culture. We examined control_shRNA-MDA-MB-231 cells and SATB1_shRNA1-MDA-MB-231 cells under two culture condition;on plastic dish(2D culture) and on Matrigel coated dish(3D culture). When SATB1 was depleted by RNAi technology, these normally aggressive cells exhibited normal breast like morphology on 3D. We used two different microarray platforms (Codelink and Affymetrix) to make expression data. Initial analysis of data and cross-platform comparison were performed using Codelink expression analysis and GeneSpring software. We provide ratio for control_shRNA/SATB1_shRNA1-MDA-MB-231 cells for 2D and 3D on this series.
2010-05-26 | E-GEOD-5417 | biostudies-arrayexpress
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2018-06-19 | GSE115947 | GEO
Project description:Background Three-dimensional (3D) bioengineered models of human skeletal muscle are a promising approach for studying muscle development, function and disease in vitro. These models more closely resemble the complexity of native muscle tissue than two-dimensional (2D) monolayer culture and allow for functional measurements to be performed. However, a more complete understanding of how culture condition and duration impacts the myotube maturity and function is required to validate the transition from 2D to 3D culture of muscle cells. Methods Human skeletal muscle cells were cultured as either 2D monolayers or within 3D fibrin-based hydrogels as muscle constructs for up to 21 days. Quantitative proteomic analysis and functional assessments, including contractile force and cross-sectional area measurements, were conducted to evaluate the impact of culture conditions and duration on muscle cell differentiation. Results Proteomic analysis revealed myoblasts differentiated into myotubes by 8 days of differentiation in both 2D and 3D environments. However, the proteomic profiles of myotubes varied significantly between the two culture environments. At day 8 of differentiation, myosin heavy chain isotype abundance indicated a predominantly slow-twitch phenotype in 3D constructs, compared to a mixed fibre type phenotype in 2D monolayers. By day 21 of differentiation, 3D muscle constructs displayed improved mitochondrial maturity, extracellular matrix remodelling, and signs of transitioning towards a fast-twitch phenotype. This prolonged culture duration also resulted in increased passive tension but decreased peak contractile force in 3D muscle constructs. Conclusions This study demonstrates that 3D culture promotes maturity in human skeletal muscle cells, mimicking the biochemical cues and energy demands seen in native muscle tissue. The data highlights the importance of selecting appropriate culture conditions and durations when studying skeletal muscle cells in vitro and suggests 8 days of differentiation as optimal for achieving peak contractile force in 3D muscle constructs.
2025-06-23 | PXD061227 | Pride