title: siMock+MyoD+Niraparib
design: For the library preparation, Hi-C experiments were performed as previously described  (Rao, S.S., et al.)  with some modifications (Vidal, E., et al.). Briefly, after cross-link with 1% formaldehyde and quenching with glycine (125 mM final), cell pellets were incubated 30 minutes on ice in 3C lysis Buffer (10 mM Tris-HCl pH=8, 10 mM NaCl, 0.2% NP40, 1X anti-protease cocktail), centrifuged 5 minutes at 3,000 rpm and resuspended in 190 uL of NEBuffer2 1X  (New England Biolabs  NEB). 10 L of 10% SDS were added and cells were incubated for 10 minutes at 65C. After addition of Triton X-100 and 15 minutes incubation at 37C, nuclei were centrifuged 5 minutes at 3,000 rpm and resuspended in 300 uL of NEBuffer2 1X and digestion was performed overnight using 400 U MboI restriction enzyme (NEB). After filling-in the generated ends with biotinylated-dATP (1.5 L of 10 mM dCTP; 1.5 L of 10 mM dGTP; 1.5 L of 10 mM dTTP; 37.5 L of 0.4 mM Biotin-dATP; 50U of DNA Polymerase I Large (Klenow) fragment in 300 uL NEBuffer2 1X; 45 minutes at 37C), ligation was performed 4 hours at 16C using 10,000 cohesive end units of T4 DNA ligase (NEB). After reversion of the cross-link, DNA was purified and sonicated to using a Bioruptor Pico (Diagenode; 8 cycles; 20s on and 60s off). Biotinylated DNA was pulled down and End-repair, A-tailing and Illumina adaptors ligation steps were performed on beads. Hi-C libraries were sequenced on a NextSeq500.