Three prime tag-sequencing of kinetically sampled Col-0 Arabidopsis leaves inoculated with the fungal pathogen Sclerotinia sclerotiorum

Three-prime tag sequencing of Arabidopsis Col-0 leaves was performed on samples collected at 0 h (uninoculated control), and at 3 h, 6 h, 12 h, and 24 h after inoculation with Sclerotinia sclerotiorum, or after mock treatment with an agar plug. S. sclerotiorum strain 1980 was cultured on Potato Dextrose Agar (PDA) plates at 22?°C. For inoculations, a 5-mm agar plug containing actively growing S. sclerotiorum mycelium was placed either at the center of a PDA plate or on the adaxial surface of leaves of 5-week-old Arabidopsis plants. The outer ring (~5 mm wide) were harvested using a scalpel and immediately frozen in liquid nitrogen. Arabidopsis plants were grown in Jiffy pots under controlled conditions at 22?°C, with a 9-hour light period at an intensity of 120?µmol/m²/s. Total RNA was extracted from ground samples using 2.5 mm glass beads and the NucleoSpin RNA PLUS kit (Macherey-Nagel), following the manufacturer's instructions. RNA quality and concentration were assessed using an Agilent Bioanalyzer with nano chips.