Published data for H3K27Ac mapping in E14.5 mouse forebrain were downloaded from the GEO database (accession no. GSE52386) (26). The H3K27Ac-covered regions were defined as >100-bp sequences with continuous base coverage of five or more reads. Peaks that were less than 250 bp apart were merged into larger peaks. Mapping data for 5hmC distribution genome wide in NPCs and neurons were obtained previously (19).

NEUROD2 ChIP-seq data from E14.5 mouse cortices were obtained from published datasets (GEO dataset: GSE67539) (38). NEUROD2 peaks were identified using customized R scripts and Bioconductor packages. NEUROD2 peaks, based on SRR1951389 and SRR1951390 files, were first identified individually using the readGAlignmentsFromBam function. Then, the common regions between these two sequence files were identified. A heatmap for NEUROD2 signal distribution across hypomethylated sites was generated on the basis of the regions ±1.5 kb from the centers of hypomethylated DMRs. Each genomic location was divided into 30 bins. The profile of NEUROD2 was obtained from SRR1951389. The heatmap was sorted by the sum of the number of reads at each analyzed region (3 kb in total).

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