We tested the relevance of an established stem-cell-derived model of trophoblast development to Toxoplasma gondii infection. Human trophoblast stem cells were cultured under conditions suitable for cytotrophoblast cells or for the differentiation into syncytiotrophoblasts, and subsequently infected with T. gondii. RNA-seq data from both mock-treated and infected cells revealed differences between cell types and their respective responses to T. gondii infection. Overall design: Human trophoblast stem cells were cultured as cytotrophoblast cells and also differentiated into syncytiotrophoblast using a differentiation medium. Cells were mock-infected or infected with T. gondii (RH-YFP strain) with a multiplicity of infection (MOI) of 5. RNA-seq was performed in order to evaluate the differences in transcriptome between both cells and the changes after infection. The experiment was designed with 3 biological replicates for each condition.