Single-cell RNA-sequencing of wildtype (ME49∆KU80) or mutant (ME49∆KU80∆BFD1) parasites under unstressed or stressed conditions

To profile cell-cycle progression and the asynchronous process of differentiation, we performed single-cell RNA-sequencing (scRNA-Seq) of T. gondii using Seq-Well (Gierahn et al., 2017). Wild-type or ∆BFD1 parasites were grown under unstressed or stressed conditions (24, 48 or 72 h), mechanically released from host cells, and analyzed. A single Seq-Well array was used for all unstressed timepoints, and two arrays were used for the 24 and 72 hour stressed timepoints.