Extended Data Fig. 5. Transplanted hCO RNA-seq comparisons to fetal and adult human cortex.

a. Left: The first principal component (PC1) calculated on gene expression (log base 2 RPKM, reads per kilobase of exon per million reads mapped) from human cortical BrainSpan samples²³ and pseudobulk (Methods) snRNA-seq samples using previously defined developmentally regulated genes³⁸. Right: PC1 values for t-hCO and hCO samples. b. The sample weights (Methods) of five neurodevelopmental transcriptomic signatures identified by Zhu et al.³⁸ across human cortical BrainSpan samples. Dashed lines denote fitted curves by LOESS regression. c. Gene set enrichment analysis (one-sided Fisher’s exact test) using the top 200 genes from each neurodevelopmental signature with significantly up-regulated (adjusted P-value < 0.05) t-hCO genes from pseudobulk GluN clusters (neurogenesis, neuronal differentiation, and synaptogenesis signatures), Astroglia clusters (astrogenesis signature), and from pseudobulk of all clusters (myelination-related signature). Line denotes Bonferroni corrected P-value of 0.05. d. Gene expression (pseudobulk and scaled) of the top 50 significantly upregulated t-hCO genes (ranked by differential expression p-value significance) for each signature. e–f. Heat maps of t-hCO (e) and hCO (f) cluster overlap by RNA-seq integration with primary human fetal cortical cell clusters^19,20. Cell cluster labels are from original studies. RG, radial glia; Cyc.prog, cycling progenitors; tRG, truncated radial glia, mGPC, multipotent glial progenitor cell; OPC/Oligo, oligodendrocyte progenitor cell/oligodendrocyte; nIPC, neuronal intermediate progenitor cell; GluN, glutamatergic neuron; CGE IN, caudal ganglionic eminence interneuron; MGE IN, medial ganglionic eminence interneuron; EC, endothelial cell; MG, microglia; Peric., Pericytes; PgG2M and PgS, cycling progenitors; IP, intermediate progenitor; oRG, outer radial glia; End, endothelial cell; Per, pericyte; vRG, ventricular radial glia; ExM, maturing excitatory neuron; ExN, excitatory neuron; ExM.U, maturing upper layer excitatory neuron; ExDp, excitatory deep layer neuron; In, interneuron. g–h. UMAP visualization of GluN cell type classification of t-hCO (g) and hCO (h) using label transfer (methods) from adult human cortical single nuclei RNA-seq reference datasets. Transfer labels from dissected cortical layers of medial temporal gyrus (MTG)²¹ shown in g and to the left in h. Right (h): transfer labels from annotated GluN subclasses from motor cortex (M1)²². I–j. Heat maps of t-hCO (i) and hCO (j) cluster overlap by RNA-seq integration with primary human adult cortical cell clusters^21,22. Cell cluster labels are from original studies. Exc, excitatory neuron; Inh, inhibitory neuron; Astro, astrocyte; Endo, endothelial cells; CT, corticothalamic cell; ET, extratelencephalic cell; IT, intratelencephalic cell; micro, microglia; NP, near-projecting; oligo, oligodendrocyte; OPC, oligodendrocyte precursor; PVM, perivascular macrophage; VLMC, vascular and leptomeningeal cells.