Affymetrixยฎ Bovine Genome Array data sets generated for 40 peripheral blood mononuclear cell (PBMC) samples from 10 African cattle (5 trypanotolerant N’Dama and 5 trypanosusceptible Boran) collected at four time points (before infection and at 14, 25, and 34 days post-infection) for a Trypanosoma congolense infection experiment.