Expression data from Skeletal Stem Cells cultured in 3-dimensional (3D) Collagen
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PROVIDER: PRJNA799008 | ENA |
REPOSITORIES: ENA
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Project description:Skeletal stem cells (SSCs) reside in a 3-dimensional extracellular matrix (ECM) compartment and differentiate into multiple cell lineages, thereby controlling tissue maintenance and regeneration. Within this environment, SSCs can proteolytically remodel the surrounding ECM in response to growth factors that direct lineage commitment. In the bone tissue, type I collagen is the most abundant ECM. The dominant type I collagenolytic proteinase found in mammals is the type I transmembrane MMP, MMP14. Therefore, SSCs from Mmp14+/+ or Mmp14-/- mice were cultured in collagen hydrogels to explore the gene expression regulated by ECM remodeling. Microarrays were used to detail the gene expression underlying ECM remodeling process in SSCs.
2022-01-21 | GSE194077 | 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. 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
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: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 (MT1) in monolayer (2D) and 3D collagen (3D Col) growth conditions. MCF-7 cells were stably transfected with either an empty vector (pcDNA3.1/Zeo) or human MMP-14 cDNA (pcDNA3.1-MMP-14/Zeo). Cells were grown for 24, 48 and 72 hours in three-dimensional (3D) type I collagen gels or in monolayer culture conditions. Cells were then lysed in TRIzol and total RNA was isolated. For each experimental condition, total RNAs isolated from 4 independant biological replicates were pooled.
2014-12-15 | E-GEOD-49595 | biostudies-arrayexpress
Project description:All mRNA was isolated after 8 hours of culture time in each of three culture conditions. (1) TCPS Plate, (2) Collagen-GAG 2 dimensional coated plate and (3) collagen-GAG three dimensional mesh.
2008-06-11 | E-GEOD-1937 | biostudies-arrayexpress
Project description: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 (MT1) in monolayer (2D) and 3D collagen (3D Col) growth conditions.
2014-12-15 | GSE49595 | GEO
Project description:Purpose: The goals of this study are to perform NGC analysis in order to compare the gene expression profiles of GMSCs cultured in 3D-collagen hydrogel and their 2D-cultured counterparts. Methods: mRNA profiles of 3D- and 2D-cultured GMSCs were generated by deep sequencing, in triplicate, using Illumina Xten. The read alignment is done using HISAT2 v.2.0.5 software with Ensembl GRCh38 genome as reference genome. Transcripts Assembly is done using StringTie v.1.3.3b software. Significant DE genes or transcripts (q-value < 0.05) were extracted by edgeR (R package) for each comparison groups. DEGs were analyzed with gene ontology enrichment analysis and KEGG by R software with clusterProfiler package. Significant GO or KEGG terms (FDR-value < 0.05) were extracted using hypergeometric distribution. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Using an optimized data analysis workflow, significant differentially expressed genes (DEGs) were defined as those with a log2 fold change (FC) ≥1 (GMSC-3D v.s.GMSC-2D) and a false discovery rate (FDR) of ≤ 1%. A total of 5588 DEGs, including 3476 upregulated and 2112 downregulated genes were identified between 3D-cultured GMSCs and 2D-cultured counterparts with a fold change ≥1.0 and p value <0.05. Altered expression of 17 genes reltaed to neural crest stem cells, mesenchymal cells, and NOTCh signaling pathways was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical cluster analysis revealed a different hierarchical clustering algorithm between 3D- and 2D-cultured GMSCs as illustrated in the Heatmap, which uncovered several as yet uncharacterized clusters of genes that may contribute to the conversion of GMSCs into neural crest stem-like (NCSC) or Schwann cell precursor (SCP)-like cells under a defined 3D-collagen hydrogel condition. Conclusions: Our study represents the first detailed comparative analysis of gene expression profiles between 2D- and 3D-cultured GMSCs, with biologic replicates, generated by RNA-seq technology. Our RNA-seq results show that GMSCs cultured in defined 3D-collagen hydrogel underwent conversion into neural crest stem-like (NCSC)/Schwann cell precursor-like (SCP) cells charcaterized by upregulation of a panel of neural crest-related genes, NOTCH signaling components, and downregulation of a panel of mesenchymal cell-related genes. We conclude that RNA-seq based transcriptome characterization would permit further dissection of complex molecular mechanisms underlying 3D collagen hydrogel-driven conversion of GMSCs into NCSC/SCP-like cells..
2021-10-19 | GSE180519 | 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
Project description:The objective of this study was to determine how TNF-a, an important proinflammatory cytokine, affects gene expression in the human annulus. Cells were grown in a 3D collagen construct for 14 days with TNF-a. mRNA was isolated and subjected to microarray. Fold changes in gene expression were determined via GeneSifer software. Human disc tissue samples were obtained from surgical disc procedures performed on patients with herniated discs and degenerative disc disease. Cultured annulus cells were grown in a 3D collagen construct with or without 10e3 pM TNF-a for a total of 14 days. Following homogenization in TRIzol reagent, total RNA was isolated and analyzed via mircoarray.
2012-10-31 | E-GEOD-41883 | biostudies-arrayexpress
Project description:Endometriotic cyst stromal cells (ECSCs) were isolated from ovarian endometriotic cyst and cultured for 48 hours in the floating three-dimensional collagen gel culture or in the conventional two-dimensional culture. Total mRNAs were extracted and subjected to gene expression microarray.
2020-07-31 | GSE136412 | GEO