Fig. 1. Outline of experimental workflow and multi-omics approaches applied to examine K13 function in this study.

The workflow illustrates the sample collection, processing, and data acquisition steps. The Dd2 laboratory-adapted parasite line and the Cam3.II clinical isolate were genetically modified at the k13 locus via zinc-finger nuclease-based gene editing to create isogenic lines with either the wild-type (WT) or mutant k13 alleles¹⁵. RNA, protein, or metabolite samples were collected for each parasite line at 6–7 time points throughout the 48 h asexual blood stage cycle in the absence of drug treatment. Synchronized K13 mutant and WT parasites were also subjected to a pulse of DHA, either at a concentration of 350 nM for 3 h (for metabolomics) or at 700 nM for 6 h (for transcriptomics), in parallel with 0.1% DMSO vehicle control. Samples were collected during DHA exposure and post drug removal. Colored arrows represent times and conditions of harvest for the different omic methods (green for transcriptomics, orange for proteomics and purple for metabolomics). Using microarray gene expression profiling and quantitative mass spectrometry-based proteomics and metabolomics, we generated global transcriptional, proteomic, and metabolomic profiles of gene-edited lines and compared the K13 mutants to their isogenic WT counterparts across the IDC.