Extended Data Fig. 1: Characterization of neuronal and astrocyte samples, properties of the latent factors.

a, Heatmap of normalized expression (logCPM) of canonical neuron marker genes in neuronal samples (n = 68). The genes are divided into clusters based on their marker identity, shown on the annotation on the right of the plot. Human cells in all cultures expressed genes characteristic for early neuronal identity. Neurons showed decreasing expression levels of neuronal progenitor marker genes and proliferative marker genes over time but had only low expression of mature neuron markers, in line with the expected early post-mitotic neuron identity. High levels of glutamatergic neuron marker SLC17A7 was observed across all time points, while GABAergic neuron marker GAD1 remained low, confirming that the neurons were predominantly excitatory. b, Heatmap of normalized expression (logCPM) of canonical astrocyte marker genes in astrocyte samples (n = 68). The genes are divided into clusters based on their marker identity, shown on the annotation on the right of the plot. Mouse cells in mono- and co-culture exhibited abundant expression of genes characteristic of astrocytes confirming the expected astrocyte identity of the cell population. c, Heatmap of Pearson correlation values of gene weights in each latent factor. d, Gene weight distributions for each latent factor. e, Boxplots of latent factor sample weights. The boxplots’ limits show the upper- and lower quartile ranges, the center lines show the median values. The whiskers show the minimum and maximum values. f, A density plot of the distribution of gene weights (n = 10848 genes) in LF2 were normally distributed with tails having the strongest positive (highest loadings) and negative (lowest loadings) association with the latent factor. g, Gene ratio of enrichment scores (ES) from GSEA of the gene weights in LF2 show an enrichment for upregulated (top) and downregulated (bottom) genes. The leading edge subset contributing most to the ES and top enrichment are marked with a dashed, red line. Genes in the respective GO terms are highlighted in the ranked order of LF2 gene weights by vertical lines on the x-axis. h, Sunburst plot displays enrichment of synaptic GO terms in the top 500 genes in LF2 from SynGO²⁵, showing that LF2 is enriched for presynaptic annotations in SynGO.