Multi-omic profiling of the developing human cerebral cortex at the single cell level

We simultaneously profiled gene expression and chromatin accessibility in 45,549 individual nuclei isolated from the human cortex across 6 broad developmental time-points from fetus to adult. Frozen human cortical brain specimens from the 6 developmental time points were homogenized and purified by FANS prior to tagmentation and partitioning into single nuclei.  8000 nuclei from each sample were subjected to the Chromium Next GEM Single Cell Multiome ATAC and Gene Expression protocol (10x Genomics), according to manufacturer’s instructions. Resulting libraries were quantified using the KAPA library quantification kit (KAPA Biosystems) and fragment sizes determined by Tapestation (Agilent). All libraries were sequenced at New York Genome Center (NYGC) using the Novaseq platform (Illumina). Fastq alignment, filtering, barcode counting, peak calling and counting of both ATAC and gene expression molecules were performed with cellranger-arc (v.1.0.0). We processed the outputs of Cell Ranger ARC using Seurat v4.013 and Signac v1.1.045 to create a multi-omic Seurat object with paired gene expression and DNA accessibility profiles for each sample. For chromatin accessibility, we used MACS246 as implemented in the function CallPeaks in Signac to call peaks from the fragment files.

Contributed by: Kaiyi Zhu, John F. Fullard, Jaroslav Bendl, Guo-Cheng Yuan, Panos Roussos

Raw data is deposited in the Gene Expression Omnibus: GSE204684

Tissue Type: human neocortex

​​Keywords: enhancer, gene regulation, single-cell, brain development, neuropsychiatric disorders.