Cell type-specific ATAC-seq data of great ape cerebral organoids and human fetal neocortex

Cell type-specific ATAC-seq data collected from human fetal cortical tissue (Gestational week 13-14) and human, chimpanzee and gorilla cerebral organoids (week 8). Data was acquired from the four major cell populations present in the developing neocortex. 50K nuclei from apical radial glia (aRG), basal radial glia (bRG), basal intermediate progenitors (bIP) and neurons (N) were isolated from tissue samples using FACS and processed for ATAC. All data was acquired in duplicate. For human tissue, independent biological replicates were acquired. For organoids, independent batches of the same cell line were processed for each species. ATAC-seq libraries were mapped and processed using the ENCODE pipeline (Lee et al. 2016) with default settings. GorGor6, panTro6 and hg38 were used as the reference genomes for gorilla, chimpanzee and human, respectively. Putative orthologous regulatory regions were identified using the HALPER tool (Zhang et al. 2020; Kaplow et al. 2023) after generating reference-free Cactus multiple sequence alignments of the gorGor6, panTro6 and hg38 genomes (Armstrong et al. 2020). The orthologous regions were merged to generate a common peak set (225,395 peaks). For each cell type and sample, we provide merged bigwig coverage files and called peaks in narrowPeak files.