Processed data and R code sufficient to reproduce the analysis in "The transcriptomic response to a short day to long day shift in the reference legume Medicago truncatula" by Thomson et al. (2019).Combines two similar experiments where plants were grown in short-day photoperiods and shifted to long-day photoperiods after 10 days. Triplicate RNA-seq libraries from both short-day and long-day leaf tissue were generated in experiment 1 at ZT0 and ZT4 at 13 days. In experiment 2 at ZT4 at 15 days.