Diamag protein a and protein g coated magnetic beads

To identify DNA-associated RNAs, human cardiomyocytes were crosslinked with UV light at 254 nm. Nuclei were isolated with the truCHIP™ Chromatin Shearing Kit (Covaris, USA) according to the manufacturer’s protocol, but without sonication. Dilution buffer (20 mM Tris-HCl, pH = 7.4; 100 mM NaCl; 2 mM EDTA; 0.5% Triton X-100; protease inhibitors) was added to lysates that were subsequently pre-cleared with 20 µl DiaMag protein A- and protein G-coated magnetic beads (Diagenode, Seraing, Belgium) for 30 min at 4 °C. The samples were incubated overnight at 4 °C with 5 µg anti-DNA-RNA hybrid S9.6 antibody^{26 (link)} (ENH001, Kerafast) or with anti-rabbit IgG control antibody (#15410206, Diagenode). Complexes were captured with 50 µl DiaMag protein A- and protein G-coated magnetic beads (Diagenode, Seraing, Belgium) for 3 h at 4 °C. Subsequently, beads were washed three times in dilution buffer, incubated with RNase H (10 units, 60 min, 37 °C; NEB M0297L), washed again in dilution buffer and treated with 1× Proteinase K (Diagenode, Seraing, Belgium). RNA was extracted using QIAzol (QIAgen), chloroform and glycogen together with 5% input.