Supplementary Figure 1: Dynamics of gene expression in YMC.

(a, b) RNA-seq experiment reveals the same three clusters (OX, RB and RC) discovered by previous microarray experiments. 3 cycles of microarray data are plotted in the first three joint columns, each containing 12 time points. 16 time-point RNA-seq data are plotted in the last joint column. (a) Enriched GO terms are labeled on the right. (b) 537 “non-cycling” genes defined previously show clearly elevated expression level in OX phase. Algorithm previously used to define cycling genes required highest expression of 2 or more time points and highest expression in all three cycle periods. As can be seen, these 537 genes form very sharp peaks with only one high time point and/or are represented in only one or two cycles. (c) Average 16 time-point RNA-seq data across genes in subclusters from Figure 1 (b-d). (d) Expression level of RTT109 and HST3 across 16 time points extracted from the RNA-seq experiment.