Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic profiling of two-dimensional cultured cells and three-dimensional dental pulp stem cell spheroids regulated by spermidine and TGF-β3

ABSTRACT: Dental pulp stem cells (DPSCs) exhibit distinct biological behaviors under conventional two-dimensional (2D) culture and three-dimensional (3D) spheroid conditions. To investigate the transcriptional regulation associated with spheroid formation and biomimetic factor-mediated functional modulation, RNA sequencing was performed on human DPSCs cultured under 2D and 3D conditions with or without spermidine (SPD) and transforming growth factor-β3 (TGF-β3) treatment. Four experimental groups, including 2D cultured DPSCs (DPSC_2D), ST-GH-treated 2D cultured DPSCs (DPSC_2ST), 3D DPSC spheroids (DPSC_3D), and ST-GH-treated 3D DPSC spheroids (DPSC_3ST), were analyzed. Transcriptomic profiling identified differentially expressed genes associated with extracellular matrix (ECM) organization, cell adhesion, angiogenesis, inflammatory regulation, and tissue regeneration. Comparative analyses revealed that 3D spheroid formation enhanced regenerative-associated transcriptional signatures, while SPD/TGF-β3 treatment further promoted ECM remodeling, angiogenic signaling, and suppression of inflammation-related pathways. These findings provide molecular insights into the regulatory effects of 3D spheroid architecture and endogenous biomimetic cues on DPSC regenerative functionality.

ORGANISM(S): Homo sapiens

PROVIDER: GSE342852 | GEO | 2026/08/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	GSE342852_gene_expression.txt.gz	Txt

Items per page:

1 - 2 of 2

Similar Datasets

Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

Project description:TGFbeta/TNFalpha treated spheroid A549 cultures are a model of the epithelial-mesenchymal transition (EMT). These experiments capture the changes in global gene expression that result from cells being induced to undergo EMT (3D control vs 3D treated), but also the differences in gene expression when A549 is grown in spheroid cultures (2D control vs 3D untreated). EMT is efficiently induced only in the spheroid culture model. A total of 8 samples are analyzed, corresponding to 4 conditions (2D control, 2D treated, 3D control, 3D treated) and 2 biological replicates.

2013-09-12 | E-GEOD-42373 | biostudies-arrayexpress

Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids

Project description:In the study of interphase chromosome organization, genome-wide chromosome conformation capture (Hi-C) maps are often generated using 2-dimensional (2D) monolayer cultures. These 2D cells have morphological deviations from cells that exist in 3-dimensional (3D) tissues in vivo, and may not maintain the same chromosome conformation. We used Hi-C maps to test the extent of differences in chromosome conformation between human fibroblasts grown in 2D cultures and those grown in 3D spheroids. Significant differences in chromosome conformation were found between 2D cells and those grown in spheroids. Intra-chromosomal interactions were generally increased in spheroid cells, with a few exceptions, while inter-chromosomal interactions were generally decreased. Overall, chromosomes located closer to the nuclear periphery had increased intra-chromosomal contacts in spheroid cells, while those located more centrally had decreased interactions. This study highlights the necessity to conduct studies on the topography of the interphase nucleus under conditions that mimic an in vivo environment.

2016-01-26 | GSE77237 | GEO

Comparative Metabolomic and Transcriptomic Analysis of Two Dimensional and Three Dimensional Mesenchymal Stem Cell Cultures for Improved Therapeutic Applications

Project description:Mesenchymal stem cells (MSCs) are widely used in regenerative medicine due to their multipotency and immunomodulatory capabilities. Compared to conventional two-dimensional (2D) monolayer cultures, three-dimensional (3D) spheroid cultures more closely recapitulate the in vivo microenvironment, influencing MSC metabolic activity and therapeutic efficacy. This study utilizes metabolomics and transcriptomics to assess and compare the metabolic activity of MSCs cultured under 2D and 3D conditions, to evaluate how these culture environments affect MSC behavior, proliferation, and function. Our findings indicate that MSCs in 3D spheroids exhibit reduced proliferation, enhanced stemness, and distinct metabolic adaptations, including increased glycolysis and alterations in nutrient metabolism. These changes promote a more quiescent state, which is favorable for tissue repair and immune modulation. Understanding these metabolic adaptations can provide valuable insights for optimizing culture conditions, improving MSCs-based therapies, and identifying novel therapeutic targets and biomarkers.

2026-02-28 | GSE290739 | GEO

Madin-Darby Canine Kidney (MDCK) cells grown in 2-dimensional and 3-dimensional type I collagen culture.

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

Expression data of two human cancer cell lines cultivated in 2-dimensional (2D) vs. 3-dimensional (3D) cell culture

Project description: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 radioresistance. Keywords: comparison of 2D vs. 3D cell culture RNA of cells was isolated four days after growing in the two different cell culture systems

2010-07-30 | E-GEOD-17347 | biostudies-arrayexpress

3D spheroid human placenta-derived mesenchymal stem cells enhances anti-inflammatory response and trophic-factors secretion

Project description:We found significant difference between the 3D-spheroid cultured- and conventionally cultured mesenchymal stem cells (3D MSCs and 2D MSCs) in terms of anti-inflammatory response and ability to secrete trophic factors, implying that 3D MSCs may better improve the tissue repair and promote functional recovery. Next-generation sequencing has revolutionized system-based analysis of cellular pathways. The aims of this study are to compare the transcriptome profile between the 3D-spheroid cultured- and conventionally cultured mesenchymal stem cells (3D MSCs and 2D MSCs).

2021-09-01 | GSE174619 | GEO

Gene expression profiling of primary human bone marrow mesenchymal stromal cells (MSCs) cultured as 2D monolayers and 3D cellular aggregates (spheroids)

Project description:Human bone marrow mesenchymal stromal cells (MSCs) are conventionally cultured as adherent monolayers on tissue culture plastic. MSCs can also be cultured as 3D cell aggregates (spheroids). Optimised 3D conditions (60,000 MSCs cultured as a spheroid for 5 days) inhibited MSC proliferation and induced cell shrinkage in the absence of cell death. Primary human MSCs isolated from 2 donors were cultured under both monolayer (2D MSCs) and optimised 3D (3D MSCs) conditions. High quality RNA was isolated from all samples, and global gene expression analysis was performed in duplicate (using Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays) to identify gene expression changes in 3D compared to 2D MSC cultures.

2015-09-30 | E-MTAB-3795 | biostudies-arrayexpress

Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

2013-09-12 | GSE42373 | GEO