Epigenome profiling identifies H3K27me3 regulation of extracellular matrix composition in human corticogenesis

Cell type-specific CUT&Tag data for H3K27me3 and H3K4me3 collected from human foetal cortical tissue (HT, Gestational week 12-14) and human cortical organoids (week 8). CUT&Tag data was acquired from the three major cell populations present in the developing neocortex. 50K nuclei from radial glia (RG), intermediate progenitors (IP) and neurons (N) were isolated from cortical tissue samples using FANS and processed for CUT&Tag. As a control 50K unstained (us) nuclei were also sorted and processed for CUT&Tag. Cortical organoid samples were treated with a Polycomb repressive complex 2 inhibitor (EED226) or DMSO from week 3 to week 8 of culture. All data was acquired in duplicate. For human tissue two independent biological replicates were acquired. For organoids two independent batches of the same cell line (CRTDi004-A (Völkner et al., 2022)) were processed. CUT&Tag bioinformatics analysis was done using the nf-core cutandrun pipeline (v3.2.2) (Cheshire et al., 2024; Ewels et al., 2020), with “--genome hg38 --macs-gsize 2805665311 --mito_name ‘chrM’ --normalization_binsize 1 --use_control ‘false’ --dedup_target_reads --peakcaller SEACR --seacr_peak_threshold 0.01” and default settings otherwise. The blacklist provided was derived from (Amemiya et al., 2019). For each sample we provide bigwig covergae files and called peaks in bed files.