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Figure S1. Principal component analysis of cardiac disease type among 448,814 loci. The segregation of β-values of 448,814 loci from 49 different cardiac tissue samples (mean values of biological replicates, for detailed information see Additional file 14: Table S1) that were subjected to 450K array DNA methylation analysis is depicted. Cardiac disease types are given in different colours and shapes: AVSD (red round dots), DCM (yellow triangles), HLHS (green solid squares), HRHS (blue crosses), LV-Aneurysm (purple squares). No differences in DNA methylation could be observed between different types of cardiac disease. (PDF 1442 kb)

Figure S8. Boxplots (t test) of 16 candidate CpG loci with differential atrial-ventricular methylation pattern. Differential DNA methylation (β-value) of 16 candidate CpG loci in atrial (n = 44) and ventricular (n = 5) cardiac tissue samples being either hypomethylated or hypermethylated in atrial tissue (coloured blue) compared to ventricular tissue (coloured red). Highly significant DNA methylation differences (p ≤ 0.0001) in atrial vs. ventricular tissues have been detected at 13 of 16 CpG loci (Welch Two Sample t test) with 9 loci displaying p values

Figure S4. Unsupervised principal component analysis of β-values from 49 cardiac tissue samples. The segregation of β-values of 2045 CpG loci (σ/σmax > 0.4) of 49 different cardiac tissue samples (IAS, LA, RA, LV, RV) that were subjected to 450K array analysis is depicted. Subgroups of atrial and ventricular samples are marked as dashed and solid edging, respectively. IAS: red spheres, LA: pink spheres, RA: green spheres, LV: blue spheres, RV: yellow spheres. Tendencies of segregation into two groups, atrial and ventricular cardiac tissues, could already be noticed in unsupervised analysis. (PDF 252 kb)

Figure S7. mRNA expression of DNA methyltransferase genes in atrial and ventricular tissues. qPCR experiments were performed on atrial (LA, RA; grey bars) and ventricular (LV, RV; white bars) tissues of one patient (0126) with LV-Aneurysm. Triplicates of cDNA samples were analysed. Expression data was normalized to GUSB housekeeping gene and compared to atrial or ventricular expression (∆∆ CT method), p

Figure S13. Bisulfite pyrosequencing analysis of candidate CpG loci: test of specificity of AVM pattern. DNA methylation patterns of different cell lines (grey bars, each single samples)—endothelial cells of the hiPSC line (hiPSC-EC), valve interstitial cardiac cell line (VIC, Innoprot P10462) and a non-cardiac cell line MCF7 (breast cancer cell line)—were investigated using bisulfite pyrosequencing technique to compare to the AVM patterns of cardiac tissues from patients with CHDs (discovery set, 450K array data of atrial (n = 44) and ventricular (n = 5) tissues; white bars) and in vitro cultivated atrial and ventricular subtypes of hiPSC-CMs (bisulfite pyrosequencing data, n = 4 atrial-like and n = 8 ventricular-like hiPSC-CMs; dotted bars). CpG loci with significant (p

Figure S13. Bisulfite pyrosequencing analysis of candidate CpG loci: test of specificity of AVM pattern. DNA methylation patterns of different cell lines (grey bars, each single samples)—endothelial cells of the hiPSC line (hiPSC-EC), valve interstitial cardiac cell line (VIC, Innoprot P10462) and a non-cardiac cell line MCF7 (breast cancer cell line)—were investigated using bisulfite pyrosequencing technique to compare to the AVM patterns of cardiac tissues from patients with CHDs (discovery set, 450K array data of atrial (n = 44) and ventricular (n = 5) tissues; white bars) and in vitro cultivated atrial and ventricular subtypes of hiPSC-CMs (bisulfite pyrosequencing data, n = 4 atrial-like and n = 8 ventricular-like hiPSC-CMs; dotted bars). CpG loci with significant (p

Figure S7. mRNA expression of DNA methyltransferase genes in atrial and ventricular tissues. qPCR experiments were performed on atrial (LA, RA; grey bars) and ventricular (LV, RV; white bars) tissues of one patient (0126) with LV-Aneurysm. Triplicates of cDNA samples were analysed. Expression data was normalized to GUSB housekeeping gene and compared to atrial or ventricular expression (∆∆ CT method), p