Fig. 1
Gene expression changes rapidly during transitions between schizont, merozoite, and ring stage parasites. A Heatmap depicting differentially expressed genes (log2(fold change) > 1.5 or < -1.5 and adjusted p-value < 0.1) between early schizont samples (40 hpi, n = 3) and merozoites (MZ, n = 3), all collected by us. Expression of these genes in early schizont (40 hpi, n = 3) and merozoite (MZ, n = 3) samples generated by Wichers et al. are shown on the right. B Principal component analysis of all RNA-seq samples. Merozoite subpopulations defined in panel C are indicated by blue numbers. Amount of variance between samples accounted for by each component is shown on the x- and y- axes. C Heatmap depicting differentially expressed genes (log2(fold change) > 1.5 or < -1.5 and adjusted p-value < 0.1) between early schizont samples (40 hpi, n = 6) and merozoites (n = 6). Genes are divided into 4 clusters based on expression pattern by k-means clustering as indicated on the left of the heatmap. Merozoite subpopulations are indicated by the labels on the bottom of the heatmap. Enriched gene ontology (GO) terms in each cluster are displayed to the right of the heatmap. D Boxplots of average gene expression for each group as shown in panel C. Gene expression differed between groups (Kruskal–Wallis test). P values indicated in the graph are from Dunn’s post hoc tests. *, P < 0.05; **, P < 0.01. For all boxplots, box edges indicate the first and third quartiles, mid-line indicates the median, and whiskers indicate the minimum and maximum data values. E H3K9ac and H3K27ac expression shown as log2(ChIP/input) around the translation start site (ATG) for genes from each group as indicated in panel C in early schizonts (40 hpi), merozoites, and early rings (4 hpi). Graphs were generated using computeMatrix from the deepTools package