GSM1215592: P.falciparum_3D7_0h_HiSeq; Plasmodium falciparum 3D7; OTHER
P. falciparum cultures were crosslinked for 25 minutes at 37C in 1.25% formaldehyde. The reaction was quenched for 15 min at 37C, followed by extensive washes to remove cellular debris. We then applied an adapted Hi-C method referred to as tethered conformation capture. Briefly, proteins were first biotinylated and the DNA was digested using the restriction enzyme MboI. Fragments were captured on streptavidin-coated beads, ligated under dilute conditions and subsequently sequenced using the Illumina HiSeq 2000 platform, generating 50 bp paired-end reads. Libraries were generated using the NEBNext ChIP-Seq Library Preparation kit (NEB) according to the manufacturer’s instructions, with the following modifications for the high AT-content of the P. falciparum genome: libraries were amplified for a total of 11 PCR cycles (3 cycles of [15s at 98°C, 30s at 55°C, 30s at 62°C] followed by 8 cycles of [15s at 98°C, 30s at 63°C, 30s at 72°C]).
GEO
GSM1215592