Fig. 2
From: Global early replication disrupts gene expression and chromatin conformation in a single cell cycle
Global early replication perturbs the expression of 27% of genes in one cell cycle. A Overlay of the flow cytometry between the sml1Δ and sml1Δ SSDDCS strains arrested in α factor and released into S-phase in galactose. The timepoints (1-12) used to generate time-resolved RNA-seq libraries are indicated. B Table showing the number of differentially expressed genes at each of the 12 RNA-seq timepoints between the sml1Δ and sml1Δ SSDDCS strains. Cells are color-coded based on the number of DE genes on each timepoint. C Heatmap of 1771 genes that are differentially expressed (DE) between the two strains in one or more timepoints after G1. Each row corresponds to one individual gene and each column to one timepoint (G1 to 60 min from left to right, respectively). Genes were clustered according to their expression profiles using k-means clustering. The expression levels were z-scored and normalized by row. The maximal and minimum expression are colored in red and blue, respectively. D Normalized read counts per timepoint using DESeq2 size factors for one illustrative gene from each DE cluster from C. E Table showing k-means clusters from C with the statistically significant (p-value <0.05) over- (blue) or under- (red) representation of genes designated to be cell cycle regulated according to [32]. p-values were calculated using binomial probability tests. F Box and whisker plot of the log2 time course-averaged expression fold-change for sml1Δ SSDDCS / sml1Δ strains of genes separated into constitutively expressed or inducible according to [33]