GSM9894641: 10E_ap2hs_3xHA_plusCHO_rep1_IP; Plasmodium falciparum; ChIP-Seq
ChIP-seq was performed using cultures at late trophozoites or early schizont stage (not tightly synchronized). Chromatin was extracted from ~60 ml at ~3-4% parasitemia as previously described, with some modifications (Llorà-Batlle, O., 2020. PMID: 32577509). Briefly, after saponin lysis and formaldehyde cross-linking, chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies, 492024). All chromatin obtained was sonicated with a Bioruptor Plus sonicator (Diagenode) as previously described (Pérez-Cantero, A., 2025. PMID: 40455742) and used for the immunoprecipitation (diluted 1:5), except for a small fraction that was used to prepare input samples. For immunoprecipitation, the anti-HA antibody at 2 μg/ml (Roche, 11867423001) was used. An equal sample was processed in parallel as input, with no immunoprecipitation. Approximately half the volume of the DNAs obtained was used for library preparation (no Qubit quantification). Library preparation was performed using 5 ng of DNA, as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). NEBNext multiplex oligonucleotides for Illumina (NEB, E7335, E7500 and E7710) were used, and 9 cycles of amplification were performed with the Kapa HiFi HotStart PCR kit (Roche, 7958889001). All purification steps were carried out using AMPure XP beads (Beckman Coulter, 082A63881). Quality and concentration of all libraries was determined using a Tapestation 4200 (Agilent). We obtained ~8-19 million 150 bp paired-end reads per sample using a NextSeq500 System (Illumina).