Given the expression of several mutually exclusive subtype markers in the bulk analysis, we investigated the expression of these genes at the single-cell level. Immunofluorescence analysis showed that ~37% of the neurons were CR-positive, 28% were CB-positive and 9% were SST-positive at 5 WPI (Fig. 2h,i and Supplementary Fig. 4). Less than 2% of the AD-iN cells were CR/SST double positive or CB/SST double positive (Fig. 2h,i). We observed expression of ISL1 in about 20% of the cells and of NR2F2 and PV in a small fraction of AD-iN cells (Fig. 2j and Supplementary Fig. 4). On the other hand, we detected exceedingly few or no CTIP2-, NKX2-1-, SP8- and DARRP-32-expressing cells.
