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Extended Data Fig. 3 | RNA and NTR velocities. a, PCA computed on
velocity values, on expression values projected 1 h into the future using
velocity and the intron/exon count ratio for the scSLAM-seq data using
the same set of genes as in Fig. 2a (uninfected, n = 2 replicates, 43 cells;
infected, n = 2 replicates, 44 cells). b, PCA for the 10x data on the same
set of genes as used for Fig. 2a on the basis of mature transcripts (exonic
reads only; left) marginally separated uninfected from infected cells. By
contrast, on the basis of the ratio of intronic/exonic reads (right), infected
cells were almost perfectly separated from uninfected (right; uninfected,
n = 2 replicates, 793 cells; infected, n = 2 replicates, 353 cells). c, As in
Fig. 2d, except velocities were computed on the basis of degradation rates
estimated from uninfected cells only; that is, not violating the steady-
state assumption but supplying the class labels (violating the blind test of
prediction). d, Scatterplot comparing NTRs with velocities from the 10x
scRNA-seq data for down- and upregulated genes.