Many Arabidopsis thaliana accession show sensitvity to the air pollutant ozone, including the accession Cvi-0 from the Cape Verde Islands. To understand and assist in genetic mapping of loci causing the ozone sensitvity of Cvi-0, transcript profiling was performed in Cvi-0, the tolerant Col-0, and a near isogenic line (Col-S) where ozone sensitivity was introgressesed from Cvi-0 to Col-0 through eight rounds of backcrossing. Overall design: The near isogenic line Col-S and its parents Col-0 and Cvi-0 were grown for three weeks and treated with 350 ppb ozone for two hours. The whole rosettas were harvested from controls and and ozone treated plants. Three separate biological repeats used for RNA-seq analysis.