scRNAseq of skeletal tissue during zebrafish craniofacial development

We used scRNAseq to characterize differentiation of cell populations during zebrafish craniofacial development. We focused critical stages during suture formation, and compared wildtype fish to mutants lacking the transcription factor sp7, that display striking abnormalities in skull and suture formation. Dissociated cells were isolated from heads of wildtype and sp7 mutant zebrafish at ~5.8 mm SL (2 weeks post-fertilization) and ~7 mm SL (3wpf). To enrich for skeletal tissues, brain and eyes were removed before dissociation. To aid in dissection and transcript analysis, fish carried two transgenes, -117BMPER: egfp and sp7: mcherry. Cells were analyzed by scRNAseq.