Fig. 7

F121 d7 and d11 cells are mostly mesodermal in nature and distinct from NPCs. A Heatmap of the topic matrix generated from non-allelic F121 sci-RNA-seq data. The color scale reflects the probability that a cell is associated with a particular topic. Topics (rows) and cells (columns) are hierarchically clustered to show relatedness. The color bar along the top of the heatmap designates cell time points with additional annotation to the heatmap to highlight topics associated with particular time points. B PCA projections (left) and UMAP (right) using the first two components of the count topic matrix used as input to the topic modeling described in A where each data point is a cell colored by time point. C UMAP as in B, but colored by the probability that cells are associated with selected d7, d11, and NPC topics used for gene ontology analysis in D. D Results of gene ontology (GO) analysis based on genes associated with the selected topics. The top 5 significant terms per topic with the highest fold change relative to all regions are plotted with circle size giving an indication of the fold change and color showing significance. Mesodermal-associated terms are highlighted in light blue with neuronal terms highlighted in gray. E–H As in A–D, but based on non-allelic F121 sci-ATAC-seq. GO analysis based on genes proximal to regions associated with the selected topics