Between 350,000 and 700,000 nuclei of Glu neurons, MGE-GABA neurons, and OLIG were isolated by flow cytometry, as described above. High-quality genomic DNA (average fragment length, >20,000 bp) was isolated using the DNeasy Blood and Tissue Kit (Qiagen) and concentrated with a Genomic DNA cleanup kit (Zymo). Genomic DNA (500 ng) was used for BS/OxBS processing and library preparation using the TrueMethyl Whole Genome kit (CEGX). Libraries were sequenced on an Illumina HiSeq 2500 system, using a paired-end 100-cycle protocol. The conversion performance in the oxidation and bisulfite treatment reactions was assessed using tailed CEGX spike-in control oligonucleotides included in the CEGX protocol. All samples passed the conversion quality control criteria suggested by CEGX (see table S3).

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