In this experiment we evaluate the transcriptional response to beet cyst nematode infection in wild-type (Col-0) and a upl3 knocked-down Arabidopsis thaliana. The data indicates that the upl3 knock-down alone does not induce a strong transcriptional regulation in the plant. However, the interaction of the mutation and infection by H. schachtii results in a strong transcriptional differential regulation, likely involving the plant’s immune responses. Samples were taken from whole root systems of 14 day-old seedlings (0 days post-infection) and mock or H. schahtii-infected 21 day-old seedlings (7 days post-infection). Each sample contained at least 18 plants and 4 biological replicates of each sample were collected.