EpiQ assay

ESC cells were grown and differentiated to EBs in 48-well plates and treated with EpiQ Chromatin Analysis kits (BioRad, Hercules, CA, USA). In this assay, heterochromatin is inaccessible to the nuclease, rendering it protected from digestion and available for subsequent quantitative (q)PCR. Cycle delays (ΔCq) with and without nuclease digestion were used to evaluate chromatin accessibility within the GNSA gDMR region. Primers for the GNSA gDMR assay are listed in Supplementary Table 3. Two other genes, constitutively expressed GAPDH and the epigenetically silenced RHO (according to the manual of the EpiQ Chromatin Analysis kit) were also included as control genes to confirm the optimal assay conditions. All qPCR runs were carried out on a ABI 7500 Fast Thermal cycler (Applied Biosystems, Foster City, CA, USA) using the EpiQ^™ chromatin SYBR^® Green supermix (BioRad, Hercules, CA, USA) after genomic DNA extraction.