GSM5456730: Pc_hypno_Mm_hepatocyte_ATAC-seq_4500; Plasmodium cynomolgi; ATAC-seq
Sorting was performed using the AriaIIIu as described previously {Voorberg-van der Wel, Elife 2021}. Parasites were collected into PBS containing 1% BSA, centrifuged (5 min, 500g, 4 °C) and kept on ice until transposase treatment. Transposase treatment was performed in 10ul volume containing 1xTD buffer (Nextera kit, Illumina), 0.5ul “home-made” Tn5 transposase adapter complex and 0.4mg/ml digitonin (Promega, #G9441) at 30 min at 37 °C. After column purification (MinElute PCR Purification Kit, Qiagen) transposed DNA fragments were PCR amplified (98 °C for 2 min; 13 cycles of 98 °C for 20 sec, 62 °C for 3 min; 62 °C for 5 min) using Nextera i5/i7 indexing primers (Illumina) and 2x KAPA HiFi HotStart ready-mix (KAPA Biosystems). The resulting libraries were subsequently purified with Agencourt AMPure XP bead (Beckman Coulter) first at 1:0.65 ratio to remove large DNA fragments, followed by addition of extra beads to the supernatant to 1:1.8 ratio and removal of adapter dimers. ATAC-seq libraries were sequenced on the Illumina NextSeq 500 system (Illumina, FC-110-3001) to generate 2x38 bp paired-end reads.
GEO
GSM5456730