GSM9257745: 10E_ap2hsKO_plusCHO_rep1_IP; Plasmodium falciparum; ChIP-Seq
ChIP-seq was performed using tightly synchronized cultures at the mid-trophozoite stage: 33–38 hpi, or 37–42 hpi for the ap2-hs KO line, to account for their slower IDC progression (Tintó-Font, E., et al., 2021; PMID:34400833), unless otherwise stated. Chromatin was extracted from ~30–45 ml at ~2% parasitemia and immunoprecipitated as previously described (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). Sonication was performed with a Covaris M220 sonicator to generate ~150–200 bp fragments. For immunoprecipitation, 2 μg of chromatin and 4 μg of anti-H3K9me3 antibody (Diagenode, C15410193) were used. An equal sample was processed in parallel as input, with no immunoprecipitation. The resulting DNA was quantified using Qubit HS before library preparation. 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).