Extended Data Fig. 4: Transcriptomic profiles of neonatal human Arc cells. | Nature Neuroscience

Extended Data Fig. 4: Transcriptomic profiles of neonatal human Arc cells.

From: An expanded subventricular zone supports postnatal cortical interneuron migration in gyrencephalic brains

Extended Data Fig. 4

a, Quality control for the snRNA-seq dataset of human Arc samples. Arc samples were collected at GW 30 and GW 39 (GW 39-1 and GW 39-2). Each dot represents a single nucleus. Nuclei with mitochondrial gene fractions above 2% were discarded in the following analysis. The GW 39-1 sample represents the more anterior level dissected at GW 39, and the GW 39-2 sample comes from the more posterior level of Arc, which is equivalent to the dissected region at GW 30. b, The distribution of the nuclei across samples visualized in UMAP space. c, The proportion of 15 clusters from three samples is shown individually. d, The gene expression profile of well-known marker genes visualized via UMAP. SOX6 and SOX11, markers of immature cells; GAD1 and DLX2, markers of GABAergic inhibitory neurons; TBR1 and SATB2, markers of excitatory neurons; OLIG2, BCAS1 and PDGFRA, markers of oligodendrocytes; SPP1 and RUNX, markers of microglia; GFAP and APOE, markers of astrocytes; PBX3, a marker of LGE-derived interneurons; HOPX, a marker for radial glia cells; CLDN5, a marker for endothelial cells; HBB, a marker for red blood cells; ERBB4 and CXCR4 are guidance receptors for the tangential migration of interneurons from the ganglionic eminence. e, Treemap showing the proportion of 15 subclusters based on gene expression. In total, 71% of nuclei express GE-associated TFs, indicating that Arc primarily harbors inhibitory populations. The dotted line includes inhibitory populations. f, Heatmap illustrating the differential gene expressions among 15 subclusters from 500 sampled cells. Radial glia cells with astrocyte characteristics (RG/AC); astrocyte (AC); glial intermediate progenitor cells (gIPC); IPC committed to inhibitory neuronal lineage (In-IPC); oligodendrocyte progenitor cells (OPC); microglia (MG); endothelial cells (Endo); immature excitatory neurons (EN); blood vessel cell (BVC); choroid plexus (CP); immature medial ganglionic eminence (Imm-MGE); caudal/lateral ganglionic eminence (CGE/LGE).

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