Combinatorial gene regulation by modulation of relative pulse timing

We performed RNAseq with Saccharomyces cerevisiae cells under both transient and steady-state conditions to study the regulation of genes by two pulsatile transcription factors, Msn2 and Mig1. The transient data allowed us to identify combinatorial targets while the steady-state data was used to study target expression dependence on the relative pulse timing between the two TFs. For transition experiments, 18 samples (3 different strains x 3 dfferent conditions x 2 biological replicates) were analyzed. For steady-state experiments, one strain was analyzed at 9 different glucose concentrations and the other strain was analyzed at one glucose condition.