Single-nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild-type and nr5a2 mutant zebrafish embryos

The functional jaw is composed of multiple connective tissues including skeletal components (bone, cartilage, and teeth), tendon, ligament, and musculature. Cranial neural crest-derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved, we profile multi-omic chromatin accessibility (snATACseq) and transcriptome (snRNAseq) of jaw mesenchyme at single-cell resolution from the developing zebrafish jaw. To profile chromatin accessibility and transcriptome in the same cell from developing jaw, we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single-cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.