Letter reSeArCH
Extended Data Fig. 2 | Half-life estimates and PCA on regulated genes.
a, Correlation between RNA half-lives estimated from bulk SLAM-seq
(n = 2 replicates). b, The fold change (FC), log 2 (MCMV/Mock), of total
RNA from bulk SLAM-seq is scattered against the log 2 -transformed
fold change of new RNA from bulk sequencing, stratified for different
RNA half-lives (average of n = 2 replicates). c, PCA on genes that are
differentially expressed in new RNA from the bulk experiments (absolute
log 2 -transformed fold change > 0.5). Top, PCA on genes with short RNA
half-lives (less than 2 h) are shown. Bottom, PCA on genes with long
RNA half-lives (more than 4 h). Left to right, PCA was performed using
total, old or new RNA, or the NTR (infected, n = 2 replicates, 49 cells;
uninfected, n = 2 replicates, 45 cells). ARI, adjusted rand index.
d, Correlation analysis of the PCA from c with the percentage of viral
reads. Pearson’s correlation coefficients and P values determined by
a t-test on Pearson’s correlation coefficient are indicated (see Extended
Data Fig. 1j) (n = 2 replicates, 49 cells).