Fig. 9

Alignment of P. falciparum cells sequenced from a conditional ap2-g knockdown line identifies cycle 2 gametocytes. a tSNE visualization of cells that cannot stably express ap2-g (−Shld) and ap2-g expression-capable cells (+Shld) after alignment by scAlign. Each cell is colored by its corresponding cluster identified in Poran et al., and clusters are numbered according to relative position in the parasite life cycle. b scAlign state variation map defined by projecting every cell from (a) into both the +/−Shld conditions, then taking the paired difference in interpolated expression profiles. Rows represent cells, ordered by cluster from early stage (top) to late stage and GC (bottom), and columns represent the 661 most varying genes. The state variation map reveals that cluster 13 is predicted to differ in expression the most between +/−Shld. The column annotations on top indicate which of the variable genes have been previously established as a target of ap2-g via ChIP-seq experiments [43] which genes have been reported as playing a role in cell cycle 2 gametocyte maturation [44] and which gene represents ap2-g. c The same state variation map of c, but zoomed in on Cluster 13 and the genes predicted to be most differentially expressed between +/−Shld. d Average per-cluster expression levels of PF3D7_0220000 reported in c, for both the +/−Shld conditions. PF3D7_0220000 is predicted to be upregulated in −Shld relative to +Shld, which is reflected in the per-cluster expression levels. e Same as d, but for PF3D7_1102500, a gene predicted to be upregulated in +Shld relative to −Shld