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. Author manuscript; available in PMC: 2022 Apr 13.
Published in final edited form as: Nature. 2021 Jun 23;595(7868):554–559. doi: 10.1038/s41586-021-03670-5

Figure 4. scATAC-seq landscape of the developing neocortex.

Figure 4.

a UMAP visualization of the scATAC-seq data for each time point. Cells are colored by the cell types predicted from integration with scRNA-seq datasets (top), and modality (bottom).

b-c URD chromatin accessibility trajectories. Root is E13.5 progenitors, tips are E18.5 final cell types (with identity-prediction score > 70%). Cells are colored by their predicted identity (b) or accessibility of marker genes (c).

d Transcription factor (TF) motifs enriched along the ATAC tree (e). Dot size shows fold enrichment, and color is average RNA expression in nearest cells in the integrated RNA and ATAC data. Motif enrichment was calculated for sequential segments of the tree, plot separation indicates the second branch-point (top). Only genes with detected expression in the corresponding scRNA-seq cells are shown. Motif enrichment for the tree tips in bottom panel.

e Accessible elements change through time. Dynamic elements that show differential accessibility across cell types were clustered within each time point (indicated with letters, insets show scaled accessibility) and connected through time. 62-85% of the common elements per cluster retained a similar pattern between E13.5 and E18.5. AP: apical progenitors, IP: intermediate progenitors, MN: migrating neurons, IN: immature neurons.