To investigate classical TSC markers in the t0 dataset we plotted the expression of Elf5, Esrrb, Cdx2, Eomes, Tead4, Sox2 in each cluster and found that clusters 0 and 3 had the highest expression levels, whereas expression of these stem cell markers was lowest in cluster 2 (Supplementary Fig. 2f). Here, CDX2 is linked to tuberous sclerosis.