whole-organism Micro-C of Oculina patagonica
O. patagonica cells were first crosslinked with 1% formaldehyde for 10 minutes, followed by quenching with 128 mM glycine. The cells were then pelleted and washed with PBS before undergoing a second crosslinking step with 3 mM DSG (Thermo Scientific, A35392) in PBS for 40 minutes. This reaction was quenched with 400 mM glycine. The double-crosslinked cells were pelleted at 4,000  g for 10 minutes, the supernatant was removed, and the pellets were frozen at 80C. For Micro-C library preparation, cells were thawed in lysis buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 5 mM MgCl, 1 mM CaCl, 0.2% NP-40, 1 protease inhibitor cocktail). Chromatin was digested with 20 U of MNase (Takara Bio, 2910A) per 1 million cells to achieve approximately 80% mononucleosome digestion. The resulting DNA ends were repaired, biotinylated, and proximity-ligated using T4 DNA ligase (Thermo Scientific, EL0012). Chromatin was then reverse-crosslinked and deproteinized. Biotinylated DNA fragments were isolated using streptavidin beads, and Micro-C libraries were prepared using NEBNext Ultra II End Repair and Ligation kits (NEB, E7546). The final libraries, comprising four biological replicates, were sequenced on a NextSeq 2000 platform in paired-end mode (2  101 bp), yielding a total of 263,962,574 reads.