Single-cell RNA-seq and single-nucleus ATAC-seq analysis of mouse embryonic tissue

To provide a higher-resolution view of the enhancer landscape of craniofacial development, we complemented our maps of human craniofacial enhancers with single cell-resolved data from mouse embryonic craniofacial tissues, with the goal to identify the cell type specificity of individual enhancers. This dataset contains single-cell RNA-seq data from mouse facial tissue isolated from e11.5, e12.5, and e13.5. It also contains single-nucleus ATAC-seq (snATAC-seq) data from mouse facial tissue isolated from e10.5-e15.5. We further explored cell type-specific enhancer activity for three craniofacial enhancers (hs1431, hs746 and hs521) using mouse transgenics followed by scRNA-seq. Pre-print available at [https://doi.org/10.1101/2023.06.26.546603](https://doi.org/10.1101/2023.06.26.546603)