For each sample, 1 x 106 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). For histone modifiacations, chromatin was sheared to mononucleosomal fragments and for HP1/Suv39h1 to 200-300 bps. Libraries were prepared according to Illumina standard protocols with external barcodes.