Single-cell profiling of cranial neural crest diversification across a vertebrate lifetime

The cranial neural crest (CNC) is a vertebrate-specific population that generates a huge diversity of derivatives, including the bulk of the connective and skeletal tissues of the head. How neural crest cells generate the appropriate cell types for distinct head regions over time remains unresolved. Here we profile RNA expression (scRNAseq) and chromatin accessibility (snATACseq) of the zebrafish cranial neural crest lineage at single-cell resolution from embryos to adults. To recover the cell heterogeneity and lineage information in the span of a life time of a fish, we collected the converted cells from embryonic stages (1.5, 2 dpf), larval stage (3, 5, and 14 dpf), juvinile stage (60 dpf), to adult stage (150 or 210 dpf). We used a cranial neural crest converted zebrafish line, -28.5Sox10:Cre;bactin:BFP-to-DsRed, to permanantly convert and label the CNCC-derived cells. The converted cells were collected and subjected to single cell sequencing for both their transcriptome and open chromatin region using Chromium platform of 10X Genomic. For biological and technical control, we include replicates for both scRNAseq and snATACseq at various stages. We include an additional line, fli1a:eGFP/sox10:dsRed, for a biological and positive control of CNCC of 1.5 dpf sample.