Fig. 1

Study design. A discovery set comprising 49 human cardiac tissue samples from paediatric patients with different congenital heart diseases (CHD) was subjected to DNA methylation analysis using Illumina Infinium HumanMethylation450 BeadChips (‘450K arrays’). Having identified significant differential methylation patterns in atrial (left and right atrium (LA, RA), interatrial septum (IAS)) and ventricular (left and right ventricle (LV, RV)) tissues, the 10% quantile of CpG loci with greatest delta β-values among the differentially methylated CpG loci (16 loci) was selected to further evaluate their reproducibility using bisulfite pyrosequencing. As verification set, 11 heart tissue samples from the initial analysis were subjected to bisulfite pyrosequencing, followed by the analysis of 13 non-failing heart tissue samples from non-transplantable donor hearts as well as 4 heart tissue samples from adult patients with heart failure (HF) (validation set n = 17). To further distinguish the cellular identity of in vitro-generated human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), batches of atrial and ventricular hiPSC-CMs (n = 12) from 2D monolayers and 3D-engineered heart tissues (EHT) were subjected to bisulfite pyrosequencing. For detailed sample information, see Additional file 14: Table S1. Credits: images partly adapted from Centers for Disease Control and Prevention, National Center on Birth Defects and Developmental Disabilities [29] and Mannhardt et al., 2016 [26]