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. Author manuscript; available in PMC: 2021 May 7.
Published in final edited form as: Nat Methods. 2020 Aug 31;17(10):991–1001. doi: 10.1038/s41592-020-0935-4

Extended Data Fig. 4. scNT-Seq enables metabolic labeling-based time-resolved RNA velocity in excitatory neurons.

Extended Data Fig. 4

a. UMAP visualization of excitatory neurons (13,511 cells, with >500 genes detected per cell) that were characterized by standard splicing kinetics-based (left) or metabolic labeling based RNA velocity (right) analyses. Cells are color-coded by time points. The streamlines indicate the integration paths that connect local projections from the observed state to extrapolated future state. The thickness of streamline indicates the magnitude of velocity. UMAP plots in lower panels (same as upper panels) show randomized velocity controls for splicing (left) or metabolic labeling (right) based RNA velocity. Permutation of velocity flows was performed by shuffling velocity for genes in each cell and then randomly flipping the sign of shuffled velocity values.

b. UMAP (same as right of a) visualization of Ex neurons colored by the average new RNA expression level (natural log transformation of (TP10K + 1)) of 24 early- (left) or 73 late-response (right) genes.

c. UMAP (same as right of a) showing Ex neurons colored by the regulon activity of three representative TFs (Jun, Mef2d, and Maff).