Extended Data Fig. 6: Diffusion Map and bulk RNA-sequencing of 72 GSCs confirms Developmental and Injury Response transcriptional states.
a, Spearman correlation between diffusion component 1 (DM1; x-axis) and principal component 1 (PC1; y-axis) cell embeddings for a subset of 14,000 GSCs (500 cells/sample). b, Diffusion Map of 14,000 GSCs. Cells coloured by PC1 cell embeddings (left; Related to Fig. 2a), scaled Developmental transcriptional program score (middle) and scaled Injury Response transcriptional program score (right). c, Spectral clustering determined GSCs (n = 72 GSC cultures) profiled with bulk RNA-sequencing separated into two stable clusters. For each cluster number (x-axis), boxplots depict 200 pairwise similarities (y-axis) (adjusted Rand index, ARI) between the solution obtained for the full dataset and random subsets of data containing 80% of samples. Box plots represent the median, first and third quartiles of the distribution and whiskers represent either 1.5-times interquartile range or most extreme value. Outliers displayed as circles. d, PCA plot of GSCs profiled with bulk RNA-sequencing colored by GSVA score for Developmental signature (n = 72 GSC cultures). Circles denote GSCs from the Developmental cluster, while triangles denote GSCs from the Injury Response Cluster. e, GSEA on differentially expressed genes between Developmental and Injury Response clusters as determined by bulk RNA-sequencing, visualized with EnrichmentMap. Similar pathways (circles) are grouped into labeled clusters (larger bubbles). Blue circles denote Injury Response associated pathways and red circles denote Developmental associated pathways. Edges (lines) denote overlap between pathways. f, Spearman correlation at the individual cell (n = 65,655) level between PC1 cell embeddings from scRNA-seq and Developmental and Injury Response gene signature scores derived from bulk RNA-sequencing.
