Two biological replicates were used for NPCs and neurons, respectively. To generate the whole-genome libraries with bisulfite-converted DNA, neuronal cell DNA (1.2 μg each) was sonicated to approximately 150–base pair (bp) DNA fragments. Then, DNA was end-repaired by using the End-It DNA End-Repair Kit (Epicentre) and linker-ligated with T4 DNA ligase [New England BioLabs (NEB)]. The ligated DNA was bisulfite-converted by using the EZ DNA Methylation Gold Kit according to the manufacturer’s instructions (Zymo Research) and amplified with Pfu Turbo DNA polymerase (Agilent). Paired-end sequencing was performed using a HiSeq2500 Illumina instrument. Between 220 and 300 million aligned paired-end reads were obtained for each sample. Data have been deposited to the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) databases (accession no. GSE101090).

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