We find that certain factors regulate the abundance of cell fates, whereas other factors affect neuronal cell states after differentiation. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoids. We developed Pando-a flexible framework that incorporates multi-omic data and predictions of transcription-factor-binding sites to infer a global gene regulatory network describing organoid development. Here we acquire single-cell transcriptome and accessible chromatin data over a dense time course in human organoids covering neuroepithelial formation, patterning, brain regionalization and neurogenesis, and identify temporally dynamic and brain-region-specific regulatory regions. Self-organizing neural organoids grown from pluripotent stem cells 1, 2, 3 combined with single-cell genomic technologies provide opportunities to examine gene regulatory networks underlying human brain development.
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