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), log₂(MCMV/Mock), of total RNA from bulk SLAM-seq is scattered against the log₂-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 log₂-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).