Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions
Abstract
:1. Introduction
2. Results
2.1. hADSCs Spheroid Formation in Microwell
2.2. Osteogenic Differentiation of hADSCs in 2D and 3D Culture Conditions
2.3. Gene Expression Profiles during Osteogenic Differentiation of hADSCs
2.4. Identification of Differentially Expressed Genes during Osteogenic Differentiation
2.5. Identification of Molecular Signature Specific to Samples in 3D Culture Condition
3. Discussion
4. Materials and Methods
4.1. Cell Culture and Osteogenic Differentiation
4.2. Concave Microwell Preparation
4.3. Generation of hADSCs Spheroids and Osteogenic Differentiation in 3D Culture Condition
4.4. Quantitative Real-Time Polymerase Chain Reaction (qRT–PCR)
4.5. Histological Analysis of 3D Spheroid
4.6. Alizarin Red Staining
4.7. RNA Sequencing (RNA-Seq) and Read Mapping
4.8. Principal Component Analysis
4.9. Differential Gene Expression (DGE) Analysis and Functional Annotations for the Differentially Expressed Genes
4.10. Time-Series Analysis of Differential Gene Expression
4.11. RNA Sequencing Validation by qRT–PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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GO Term | GO Term ID | Gene Count | p-Value |
---|---|---|---|
extracellular matrix organization | GO:0030198 | 23 | <0.0001 |
skeletal system development | GO:0001501 | 17 | <0.0001 |
angiogenesis | GO:0001525 | 16 | 0.0003 |
osteoblast differentiation | GO:0001649 | 11 | <0.0001 |
BMP signaling pathway | GO:0030509 | 10 | <0.0001 |
embryonic limb morphogenesis | GO:0030326 | 10 | <0.0001 |
cartilage development | GO:0051216 | 10 | <0.0001 |
collagen fibril organization | GO:0030199 | 9 | <0.0001 |
embryonic skeletal system morphogenesis | GO:0048704 | 9 | <0.0001 |
odontogenesis of dentin-containing tooth | GO:0042475 | 9 | 0.0001 |
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Kim, B.-C.; Kwack, K.H.; Chun, J.; Lee, J.-H. Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions. Int. J. Mol. Sci. 2021, 22, 7939. https://doi.org/10.3390/ijms22157939
Kim B-C, Kwack KH, Chun J, Lee J-H. Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions. International Journal of Molecular Sciences. 2021; 22(15):7939. https://doi.org/10.3390/ijms22157939
Chicago/Turabian StyleKim, Byung-Chul, Kyu Hwan Kwack, Jeewan Chun, and Jae-Hyung Lee. 2021. "Comparative Transcriptome Analysis of Human Adipose-Derived Stem Cells Undergoing Osteogenesis in 2D and 3D Culture Conditions" International Journal of Molecular Sciences 22, no. 15: 7939. https://doi.org/10.3390/ijms22157939