RNA-Seq time-course of young tomato seedlings in heat stress

Seedlings of Moneymaker were grown on MS media (4.4g MS media per L, 9g Agar, using DI/Milli-Q water, pH adjusted to 5.7 using NaOH) in boxes in a plant growth chamber (Polyklima, M4Z-TDLPLUS-FarRed) at 7000 Lux, 50% relative humidity, 25C 12h day/night cycle for 7 days. Then heat stress treated plants were exposed to 37C at the beginning of a light phase and sampled after 1, 4, 8, 12, 13, 16, 20, 24, and 25 hours (hence time points 13 - 24 were sampled in the dark). Whole seedlings were harvested and flash frozen in liquid nitrogen and stored at -80C. RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Netherlands) following the manufacturer's protocol and DNA digested using the RNase-Free DNase Set (Qiagen, Netherlands). RNA-seq libraries were prepared using TruSeq library kits (Illumina, USA). RNA was sequenced using 75bp paired-end sequencing on a NextSeq 550 (Illumina, USA).