Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids
Abstract
:1. Introduction
2. Materials and Methods
2.1. Culture of Pluripotent Stem Cells
2.2. Engineering Cell Reporters
2.3. Generation of Retinal Organoids
2.4. Flow Cytometry
2.5. Sample Collection
2.6. Preparation and Imaging of Sectioned Organoids
2.7. qRT-PCR
2.8. Nuclei Isolation and ATAC-seq Libraries
2.9. RNA Isolation and RNA-seq Libraries
2.10. ATAC-seq and RNA-seq Data Analyses
3. Results
3.1. Generation of a Dual Fluorescent Reporter hPSC Line for Tracking Retinal Development
3.2. Chromatin Accessibility and Gene Expression Changes during the Stem Cell to Retinal Organoid Transition
3.3. Signaling Pathways during Optic Vesicle Differentiation
3.4. Molecular Differences during Early Retinal Cell Specification
3.5. Motif Discovery and Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Jones, M.K.; Agarwal, D.; Mazo, K.W.; Chopra, M.; Jurlina, S.L.; Dash, N.; Xu, Q.; Ogata, A.R.; Chow, M.; Hill, A.D.; et al. Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids. Cells 2022, 11, 3412. https://doi.org/10.3390/cells11213412
Jones MK, Agarwal D, Mazo KW, Chopra M, Jurlina SL, Dash N, Xu Q, Ogata AR, Chow M, Hill AD, et al. Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids. Cells. 2022; 11(21):3412. https://doi.org/10.3390/cells11213412
Chicago/Turabian StyleJones, Melissa K., Devansh Agarwal, Kevin W. Mazo, Manan Chopra, Shawna L. Jurlina, Nicholas Dash, Qianlan Xu, Anna R. Ogata, Melissa Chow, Alex D. Hill, and et al. 2022. "Chromatin Accessibility and Transcriptional Differences in Human Stem Cell-Derived Early-Stage Retinal Organoids" Cells 11, no. 21: 3412. https://doi.org/10.3390/cells11213412