Whole Genome Sequencing of AP2-LT+3xHA Plasmodium falciparum Parasite Line

This parasite line was generated using CRISPR-Cas9 and double homologous recombination to insert a 3xHA epitope tag to the 3`-end of the pfap2-lt (PF3D7_0802100) gene from Plasmodium falciparum (wild-type 3D7 background). The parasite line was cloned out using limited dilution cloning and taken off of drug selection (2.5nM WR99210) after verification of gene modification by PCR. The sample for whole genome sequencing (WGS) was prepared by lysing asynchronous parasites with 0.1% saponin for 10 minutes at room temperature followed by washes with 1xPBS to remove lysed erythrocyte material. Genomic DNA was then purified using the Qiagen DNeasy Blood and Tissue kit with no modifications and sequenced on the Illumina HiSeq 2500 using single-end adaptors. This modified line was used to identify the genome-wide binding sites of the sequence-specific transcription factor AP2-LT, using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq). The ChIP-seq experiments were carried out on synchronized asexual blood stage parasites at 40hpi (hours post invasion) [schizont stage].