Chromatin Interaction Changes during the iPSC-NPC Model to Facilitate the Study of Biologically Significant Genes Involved in Differentiation
Abstract
:1. Introduction
2. Methods and Materials
2.1. iPSC Cells Culture and Generation of iPSC-Derived Neural Progenitor Cells
2.2. iPSC and iPSC-Derived Neural Progenitor Cells Immunofluorescence Staining
2.3. Quantitative PCR
2.4. Hi-C Data Processing
2.5. Topologically Associated Domain Calling
2.6. Differentially Interacted Region Calling
2.7. mRNA-Sequencing Data Processing
3. Results
3.1. Interaction Patterns upon NPC Differentiation from iPSC on Genomic and Domain Levels
3.2. Analysis of Topologically Associated Domains
3.3. Differentially Interacted Regions during NPC Differentiation
3.4. Role of Promoter–Promoter Interactome in Cell Fate Specification
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Choi, W.-Y.; Hwang, J.-H.; Lee, J.-Y.; Cho, A.-N.; Lee, A.J.; Jung, I.; Cho, S.-W.; Kim, L.K.; Kim, Y.-J. Chromatin Interaction Changes during the iPSC-NPC Model to Facilitate the Study of Biologically Significant Genes Involved in Differentiation. Genes 2020, 11, 1176. https://doi.org/10.3390/genes11101176
Choi W-Y, Hwang J-H, Lee J-Y, Cho A-N, Lee AJ, Jung I, Cho S-W, Kim LK, Kim Y-J. Chromatin Interaction Changes during the iPSC-NPC Model to Facilitate the Study of Biologically Significant Genes Involved in Differentiation. Genes. 2020; 11(10):1176. https://doi.org/10.3390/genes11101176
Chicago/Turabian StyleChoi, Won-Young, Ji-Hyun Hwang, Jin-Young Lee, Ann-Na Cho, Andrew J Lee, Inkyung Jung, Seung-Woo Cho, Lark Kyun Kim, and Young-Joon Kim. 2020. "Chromatin Interaction Changes during the iPSC-NPC Model to Facilitate the Study of Biologically Significant Genes Involved in Differentiation" Genes 11, no. 10: 1176. https://doi.org/10.3390/genes11101176
APA StyleChoi, W.-Y., Hwang, J.-H., Lee, J.-Y., Cho, A.-N., Lee, A. J., Jung, I., Cho, S.-W., Kim, L. K., & Kim, Y.-J. (2020). Chromatin Interaction Changes during the iPSC-NPC Model to Facilitate the Study of Biologically Significant Genes Involved in Differentiation. Genes, 11(10), 1176. https://doi.org/10.3390/genes11101176