Extended Data Fig. 8: B-scores reflect stochastic transcriptional activity in single cells.

a, Comparison of B-scores (from n = 2 replicates, 45 cells) with bulk RNA expression levels stratified by RNA half-life. The r² values of ordinary linear regression are shown (lines indicated). Especially for genes with short-lived transcripts, there was no correlation indicating that high B-scores are not due to inefficient RNA capture. b, Pearson’s correlation coefficient of NTR values for the top 10% most-variable genes for pairs of cells (n = 2 replicates, 45 cells) either in the same cell-cycle phase (purple), or in different stages of the cell cycle (green). c, Cells (n = 2 replicates, 45 cells) were ordered according to the cell cycle using reCAT (recover cycle along time)²⁷ (x axis). The correlation of each cell with the next cell in the order, or the cell farthest away in the order (opposite), is shown. Pearson’s correlation coefficients were computed on the NTR values of the top 10% most-variable genes. d, Heat map showing the NTR values for marker genes of the S and G2/M phases of the cell cycle. Grey fields indicate undetected genes. Cells (columns, n = 2 replicates, 45 cells) were ordered according to the log odds (on–off versus S–G2/M). The log odds and associated P values (two-sided Fisher’s exact test, corrected by Benjamini–Hochberg) are indicated. Genes (rows) were ordered according to the correlation of their NTR values with the log odds order. e, Distribution of the Spearman correlation coefficient of the top 10% most-variable genes (B-score against cell-cycle log-odds order; see d). For the sake of comparison, cells were permuted randomly 100 times, and the corresponding distributions of the correlation coefficient are indicated. f, Scatter plot of RNA half-lives and the fraction of on cells (n = 2 replicates, 45 cells) among all cells with the gene in either on or off state. All box plots are as in Fig. 4c. Dots denote outliers.