Quantification of expression homeostasis during DNA duplication

In order to investigate gene expression buffering, we adopted a quantification method from a previous study with slight modifications. Briefly, 500 early and 500 late replicated genes 17 were selected for quantification of transcript level abundance. For RNA-seq data from different time-points, the regulated genes, which were defined by Voichek et al. (2016), and the gene expression values with TPM <= 1 were excluded in subsequent steps. Next, the expression level of each gene at every time-point was divided by its signal in G1 phase and then log2 transformed. To calculate the average signal, the expression levels were averaged separately over early and late replicated genes for each time-point. The "% Signal early vs. late" value was calculated by dividing the average early and late signals at each time-point and multiplying by 100.