This study evaluates the transcriptome of Arabidopsis thaliana seedlings (Col-0 ecotype) treated with methyl jasmonate (MeJA) or with the salicylic acid analog benzothiadiazole (BTH). Overall design: Two-week-old Arabidopsis thaliana seedlings (Col-0 ecotype) grown under short day conditions (9h of light at 21°C - 15h of dark at 18°C) were sprayed with 50 µM MeJA (Sigma), 300 µM BTH (Actigard 50WG) or a mock solution (0.02% Silwet, 0.1% ethanol). Samples were harvested 1h, 5h and 8h after spraying and used for RNA extraction and Illumina sequencing. The experiment includes two independent biological replicates per condition. Each replicate corresponds to approximately 30 seedlings grown in the same pot.