Letter reSeArCH
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 r^2
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.- Liu, Z. et al. Reconstructing cell cycle pseudo time-series via single-cell
transcriptome data. Nat. Comm. 8 , 22 (2011).