MRA-1250 untreated parasites
To capture the transcriptome of Plasmodium single cells and generate single cell libraries, we utilized Seq-Well, a massively parallel, low-input scRNA-seq platform36,37. Briefly, 10-15,000 Pf infected RBCs from each time point and treatment condition were loaded onto a functionalized polydimethylsiloxane (PDMS) array preloaded with uniquely barcoded mRNA capture beads (Chemgenes; Macosko-2011-10(V+)). The cDNA libraries were then fragmented and amplified for sequencing using the Illumina Nextera XT DNA Library Preparation kit (Illumina, FC-131-1096) using custom primers that enabled the specific amplification of only the 3 ends. The libraries were purified, quantified, and then sequenced on a NextSeq550 system using High output 75 cycle kits (Illumina) at an average of 20,000 reads per cell. Read 1 has 21bp (containing a 12bp cell barcode and a 9bp UMI), while Read 2 has the 50bp transcript sequence.