ATAC-seq of Plasmodium falciparum: wild type 10hpi
ATAC-seq library preparation used in this manuscript was based on the published ATAC-seq method with some fine-tuning modifications [Toenhake, C. G. et al. Cell Host and Microbe 23, 557569.e9 (2018).]. In brief, 1x105 highly synchronized parasites of different stage (10 hpi, 20 hpi, 30 hpi, 40 hpi) were lysed with 0.1% saponin in 1 x PBS. Then the lysed parasites were isolated and washed once with 1xPBS, and permeabilized with 50 L cold ATAC-Resuspension Buffer (ATAC-RSB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% digitonin) for 3 min on ice. Followed by adding 1 ml wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20), the mixture was spun at 1800 g for 5min to remove the supernatant. The pellet proceeded to transpose immediately by adding 50 L transposition mixture containing 25 L 2 x TD buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 20% dimethyl formamide), 2.5 L transpose (100 nM final), 16.5 L 1xPBS, 0.5 L 1% digitonin, 0.5 L 10% Tween-20 and 5 L H2O. Reactions were incubated at 37  for 37 min with continuous mixing and cleaned up with E.Z.N.A Cycle Pure Kit (OMGA D6492-02) after incubation. Libraries were amplified using KAPA HiFi Hotstart Ready Mix (2X) (KM2612) with following PCR condition: 72  for 5 min; 98  for 30 s; 13 cycles of 98  for 20 s, 62  for 3 min; following by 62  for 5 min. Finally, libraries were purified using 1.8xAMPure (Beckman). Each library was sequenced by illumina HiSeq X Ten platform to obtain 2x150 bp reads.