Fluctuating freezing experiments (Figs. 1B–E, 3H,I; Supplemental Fig. S3F–J)

Col FRI seeds were sown onto soil. Nonvernalized plants were grown for 10 d in the nonvernalizing growth chamber and sampled at six time points over 24 h before plants were then moved to 8-h light/16-h darkness growth chambers for vernalization Light was on from 09:00 to 17:00. For vernalization, plants were treated with three different temperature regimes: constant 5°C, daily fluctuating 5°C (3°C–9°C) and daily fluctuating 5°C (−1°C to 12°C) (Fig. 1B). Three biological replicate samples were taken at six time points over 24 h after 2-wk exposure to vernalization. For the NV samples, plants were sampled at 12:00, 16:00, 20:00, and 24:00 and at 08:00 twice 24 h apart. For the vernalization samples, plants were sampled at 12:00, 16:00, 20:00, and 24:00 and at 09:00 twice 24 h apart. Lights came on at midnight for NV and at 09:00 in vernalization treatments. For Figure 3, H and I, experiments were performed as described above, except sampling was performed at the time point (09:00). For Supplemental Figure S3, F–J, experiments were performed following the above procedures, except that Col FRI seeds were sown onto medium in Petri dishes and were sampled at the time point (09:00).