Transcriptome profiling of genetically modified P. falciparum parasite strains with distinct drug resistance phenotypes

We compared the transcriptomic profiles between P. falciparum strains displaying mutant or wild-type pfcrt or varying in pfcrt or pfmdr1 expression levels All values were normalized using a background pool constituted of 11 transcriptome data sets that constituted a baseline for gene expression fold change and gene set enrichment. In addition to that reported in the present study, the pool included two IDC transcriptome data sets generated for Dd2 parasites pressured long-term with pulses of dihydroartemisinin (the 3b1 line) and the non-pressured parent (Lisewski et al., Cell, 2014), as well as the transcriptome data set previously reported for the 3D7, Dd2 and HB3 strains (Bozdech et al., PLos Biol 2003, Llinas et al, NAR 2006) We conducted gene expression microarrays over the course of the parasite 48-hr IDC, by sampling parasites every 6-hour, representing 8 different time points. Extracted RNA was labeled with Cy5 dye, while the reference RNA pool consisted of Cy3-coupled cDNA samples prepared from RNAs representing all developmental stages at 6-hour intervals of the IDC of the 3D7 line.