Figure 2—figure supplement 1.

(A) Fish transgenic for sox10:cre and ubi:loxP-EGFP-loxP-mCherry permanently and robustly expressed mCherry in NC-derived cells of both euthyroid and hypothyroid fish (Kague et al., 2012; Mosimann et al., 2011). At superficial layers, mCherry+ xanthophores (yellow arrowheads), melanophores (red arrowheads), and iridophores (blue dotted line) were apparent. At deeper layers, mCherry+ cells were found in dorsal root ganglia (magenta arrowheads) and other locations (e.g. mint arrowheads), potentially representing glia, neurons, progenitors and other cell types. mCherry+ cells of non-NC origin were evident as well (see Figure 2—figure supplement 2). Stage shown is 9.8 SSL (Parichy et al., 2009). (B) Single-cell RNA-Seq (scRNA-Seq) experimental design. To ensure that progenitors, cells at intermediate states of specification and commitment, and fully differentiated cells were captured, euthyroid and hypothyroid fish were collected at a range of stages encompassing adult pattern formation (7.2–9.8 SSL) and from juvenile fish (11 SSL) in which the first two adult stripes had fully formed. To compare transcriptomic signatures of NC-derived cells from embryonic–early larval and middle larval–juvenile stages, cells were additionally collected from euthyroid larvae at 5 dpf (3.5 SSL). (C) Representative FAC sort for NC-derived cells from post-embryonic skins and trunks. Single cells were isolated by sequentially gating cells according to their SSC-A vs. FSC-A, FSC-H vs. FSC-W, and SSC-H vs. SSC-W profiles according to standard flow cytometry practices. Cells with high levels of DAPI staining were excluded as dead or damaged. NC-derived cells were isolated by identifying cells with high fluorescence in the mCherry-A channel which describes expression of the ubi:loxP-EGFP-loxP-mCherry transgene after permanent conversion to ubi:mCherry upon exposure to sox10:Cre (see Figure 2—figure supplement 1A).