Genes selected for detailed methylation level analysis. Methylation levels were visualized for four methylated genes (columns) in both libraries (upper row: MEBS-PE_1, lower row: MEBS-PE_2). Those genes were genes known to be methylation-regulated such as the Brain-derived neurotrophic factor (Bdnf), and Peroxisomal proliferator-activated receptor alpha (Ppara) as well as the two imprinted genes Paternally expressed imprinted gene 10 (Peg10) and Insulin-like growth factor 2 (Igf2). Low (0-40% in green), intermediate (40-60% in black) and high methylation levels (60-100% in red) were shown for both strands, according to their coverage. Annotated positions (see Scaffold row) for genes (exon, introns) and CGI are depicted in the middle row. The CGIs row is divided in two sections: the lower section contained CGIs (black lines) which were calculated by the percentage of CG dinucleotides, depicted in the upper section as frequency graph. Dense high peaks represented high CG frequency, indicating CGIs. Genes were annotated as exons (thick bars) and introns (thin bars). In Igf2, the co-located and co-regulated miRNA (blue bar) was shown above the second intron. Inter-library differences were minor, but can be seen e.g. for Ppara (arrow) where methylation levels were detected only in MEBS-PE_1.