FASTQ data files were trimmed to remove adapters and low-quality reads using Scythe and Sickle software tools (https://github.com/vsbuffalo/scythe and https://github.com/najoshi/sickle) and aligned to the hg19 human genome using STAR (55). Non-uniquely mapped and duplicate reads were removed with SAMtools (58) and Picard (http://broadinstitute.github.io/picard/). Alignment files were sorted by read name, and peaks were called using the DFilter software package (59), with command line parameters based on software suggestions for each histone mark. For each sample, a matching input control was included. For H3K27me3 data sets, the following command line parameters were used: “-f=bam -pe -ks=20 -lpval=3 -nonzero”, resulting in 21,000 to 29,000 peaks per sample. For H3K27ac data sets, peaks were called with DFilter using the following parameters: “-f=bam -pe -ks=60 -lpval=4”. For each cell type, H3K27ac peak lists for replicate samples were then overlapped using a custom R script, and peaks that were present in at least half of replicates were preserved for further analysis (peak numbers: 44,519 in MGE-GABA neurons, 46,580 in Glu neurons, and 45,963 in OLIG cells). Peaks detected in Glu, MGE-GABA, and OLIG cells were further overlapped using the bedtools package (60) to obtain Glu-specific (19,697), MGE-GABA–specific (16,297), OLIG-specific (26,975), and common (12,549) peaks, as well as the peaks present in two of three cell types. ChIP-seq enrichment score in a particular region was defined as log2 (RPM pulldown/RPM input) (RPM, reads per million).

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