Extended Data Fig. 1: Identification of human-specific progenitors in motor neurogenesis.
From: A human-specific progenitor sub-domain extends neurogenesis and increases motor neuron production

(a) Culture conditions for motor neuron differentiation. (b) UMAP of all high-quality single-cell RNA-seq profiles after removal of interneuron-lineage/fibroblast-like cells, colored based on replicate. (c) Timestamp distribution in human single-cell gene expression datasets across the two replicates, normalized by cell cluster (day 10 cells in replicate 1 were not timestamped and therefore inferred based on absence of timestamp expression; see Methods) (d) Timestamp distribution (day 4–6) in mouse single-cell gene expression datasets across the two replicates. (Day 7 was not collected for first replicate.) (e) UMAP of all high-quality single-cell RNA-seq profiles, clusters colored based on identity. (f) UMAP of combined human and mouse single-cell gene expression profiles following CCA-mediated integration, colored by normalized expression level of key marker genes. (g) Chi-square distance between human and mouse clusters. Smaller distances indicate greater similarity in constituent cells’ distribution across common clusters. (h) Classification of human (top) and mouse (bottom) cells according to human-based random-forest classifier shows that the vast majority of mouse cells classified as H0-2 (pMN), H6 (late-appearing NKX2-2+/OLIG2+), or H7-9 (MN), leaving the H3-5 (vpMN) category void of classified mouse cells. (i) Macaque iPSC cultures display NKX2-2 and OLIG2 co-expressing cells when ISL1+ MNs begin to appear, mimicking human cultures (scale bar = 50μm). (j) UMAP of scRNA-seq data from Carnegie Stage 12 human embryonic spinal cords30, colored based on cluster identity or NKX2-2/OLIG2 expression. (k) Left: Alignment of human in vitro and human CS12 embryonic scRNA-seq data shows that human-specific clusters map onto distinct clusters found in vivo. Right: Alignment of human in vitro and mouse E9.5-10.5 spinal cord shows that H4 cells show poor overlap with all embryonic mouse clusters, suggesting that H4-like cells are found in human (but not mouse) embryonic spinal cords. (l) Normalized expression levels of key marker genes in CS12 human (top) and E9.5-E10.5 mouse (bottom) clusters. (m) Alignment of human in vitro and human CS14/pcw5 (CS14) embryonic scRNA-seq data. (n) Normalized expression levels of key marker genes in CS14/pcw5 human clusters.