SMF-ONT in S2 and OSC Drosophila cell lines

Collection of 2 biological replicates of SMF-ONT performed in S2 and OSC cell lines. The footprinting protocol was adapted from Kleinendorst and Barzaghi et al., 2021 and optimised for long-read sequencing and high weight DNA extraction. In summary, 2.5 million intact nuclei per SMF reaction have been treated with successive incubation with GpC (M.CviPI) and CpG (M.SssI) methyltransferase enzymes. Footprinted DNA was extracted using the Quick-DNA HMW MagBead kit following the manufacturer protocol and using wide-bore tips. Nanopore ligation library (LSK109 or LSK114) preparation has been performed using 1µg of purified footprinted HWM DNA. Sequencing has been performed using GridION flow cells for the R9 chemistry (LSK109) and promethION flow cells for the R10 chemistry (LSK114). The data have been analysed using the SMF-ONT nextflow pipeline (https://git.embl.de/grp-krebs/nf-smfont) using custom methylation call models.