In contrast to the distinct boundaries between subtypes, we also observed continuous variation in gene expression.15,16,56 On a large scale, continuos variation in gene expression was exemplified by the dorso-ventral gradients of CRYM and CNR1 (Figure 3), but there were also axes of continuous variation within and between MSN subtypes. We examined this variation using archetypal analysis.28-30 Archetypes have biologically interpretable dimensions and concepts, in genes and cell states, respectively. Moreover, projecting archetypes learned in one biological replicate onto another biological replicate requires only a simple matrix operation. This simplicity enabled us to clearly demonstrate the similarity between the biological replicates (Figure S3G). Within most of the MSN subtypes, we observed several archetypes. For example, archetypal analysis of the matrix clusters revealed an archetype that highlighted VS derived nuclei (Figure S3H). Some of the genes correlated with this VS archetype are upregulted in the NAc core.31 Thus, this archetype analysis defined a potential NAc core signal. One challenge that remains is to determine whether archetypes indicate subtypes or ‘states,’ with the former being a stable feature found across individuals and
