A single-cell and spatial 3D multi-omic atlas of developing human basal ganglia and inhibitory neurons

Heffel, Matthew G.1; Xu, Heng2; Pastor-Alonso, Oier3; Li, Xinzhe4; Baig, Mohammed S.1; Ghoor, Rayyan Irfan1; Li, Runjia1; Kern, Colin 2 ; Kum, Joonho1; Zhang, Yi1; Paino, Jon1; Tsai, Min Jen1; Tai, Chu-Yi2; Tucker, Grant2; Zhao, Zoey2; Hou, Angie2; Behren, Zachary von1; Bhade, Mohini3; Li, Siqian3; Sandoval, Kadellyn3; Scholes, Jessica1; Codrea, Felicia1; Calimlim, Jeffrey1; Liao, Emma K.1; Leung, Gwyneth1; Kim, JaeYeon3; Eskin, Eleazar1; Flint, Jonathan1; Cotter, Jennifer A.5; Pasaniuc, Bogdan4; Bintu, Bogdan2; Zhu, Quan2; Mukamel, Eran A.2; Ernst, Jason1; Paredes, Mercedes F.3; Luo, Chongyuan2

Published Apr 21, 2026 on Dryad. https://doi.org/10.5061/dryad.3tx95x6wd

Data files

Apr 21, 2026 version files 16.25 GB

Abstract

The human basal ganglia (BG), subcortical nuclei fundamental to motor regulation and cognitive modulation, is constructed from neurons produced during gestation in the adjacent ganglionic eminences (GEs). GEs are transient structures in the ventral prenatal brain that also generate GABAergic inhibitory neurons, which migrate to destinations in the BG, cortex, and other destinations. This study aims to elucidate the epigenomic and 3D-genomic dynamics involved in the specification and maturation of GEs and GE-derived neurons, using single-nucleus methyl-3C sequencing (snm3C-seq), highly-multiplexed spatial transcriptomics, and chromatin+RNA single-molecule imaging. Our multi-modal data support a heterogeneous temporal progression across GE subregions, with the lateral GE (LGE) showing declining neurogenic activity in mid-gestation and caudal GE (CGE) exhibiting ongoing developmental progression through infancy. We identified regulatory programs that specify subtypes of BG principal cells, medium spiny neurons (MSN), via synchronized maturation of the 3D-epigenome. In infant brains, we found a transient short-range enriched (SE) chromatin conformation during the transition between oligodendrocyte progenitors (OPCs) and oligodendrocytes (ODCs), and a temporary shift toward Long-range Enriched (LE) chromatin conformation in projection neurons, extending previous works showing the differentiation of neurons and glial cells is associated with permanent SE and LE conformation, respectively. Lastly, we found that gene regulatory regions active in MSNs were enriched in loci associated with genetic risk for neuropsychiatric disease. Our study delineates the highly complex, lineage-specific 3D genomic dynamics in ventral progenitors and basal ganglia populations of the perinatal human brain.

Dataset DOI: 10.5061/dryad.3tx95x6wd

Description of the data and file structure

The basal ganglia were collected at 23GW (mid-gestation) and 42GW (late-gestation). A section from each was imaged with MERFISH+ to measure expression of 463 genes, and a smaller portion of a second section was imaged with the same 463 genes as well as a region of DNA. For the 23GW sample, the NKX2.1 locus was imaged at 10kb genomic resolution, while in the 42GW sample, the DRD2 locus was imaged at 30kb genomic resolution.

Files and variables

File: D164_GW23_CT.h5ad

Description: Imaging of 463 genes using MERFISH and 39 10kb regions around the NKX2.1 genomic locus. AnnData object containing the following information for each cell: The number of genes ('n_genes_by_counts') and transcripts ('total_counts') detected, cell type annotation ('celltype'), chromatin imaging information for up to 4 chromosomes per cell. Chromatin tracing data is stored in the .obsm['X_h_score'] matrix, which is an Nx4x39x5 matrix where N is the number of cells, 4 is the maximum number of chromosomes per cell, 39 is each of the chromatin regions imaged, and 5 are the 5 properties measured for each region: The z, x, and y coordinates of the region (in microns), the brightness, and the score (see methods).

File: D166_GW42_CT.h5ad

Description: Imaging of 463 genes using MERFISH and 24 30kb regions around the DRD2 genomic locus. AnnData object containing the following information for each cell: The number of genes ('n_genes_by_counts') and transcripts ('total_counts') detected, cell type annotation ('celltype'), chromatin imaging information for up to 4 chromosomes per cell. Chromatin tracing data is stored in the .obsm['X_h_score'] matrix, which is an Nx4x24x5 matrix where N is the number of cells, 4 is the maximum number of chromosomes per cell, 24 is each of the chromatin regions imaged, and 5 are the 5 properties measured for each region: The z, x, and y coordinates of the region (in microns), the brightness, and the score (see methods).

File: R193_GW42_MERFISH.h5ad

Description: Imaging of 463 genes using MERFISH+ in a GW42 basal ganglia section. AnnData object containing the following information for each cell: The number of genes ('n_genes_by_counts') and transcripts ('total_counts') detected, and cell type annotation ('celltype').

File: R186_GW23_MERFISH.h5ad

Description: Imaging of 463 genes using MERFISH+ in a GW23 basal ganglia section. AnnData object containing the following information for each cell: The number of genes ('n_genes_by_counts') and transcripts ('total_counts') detected, and cell type annotation ('celltype').

Code/software

These files are in anndata format, which can be loaded in Python using the Scanpy package:

!pip install scanpy
import scanpy as sc
adata = sc.read("Fig1_FirstImaging.h5ad")