Single nuclei chromatin profiles of midbrain from genetically distinct mouse strains reveal cell identity transcription factors and cell type-specific gene regulatory variation

Here we report 20 658 single nuclei chromatin accessibility profiles of ventral midbrain cell types from two genetically diverse and commonly used mouse strains, C57BL6/J and A/J. In total we identify over 260 000 unique accessible sites. The distinct chromatin profiles are consistent with gene expression levels from single cell RNA-seq data and can distinguish ten midbrain cell types. Transcription factor (TF) binding motifs enriched at accessible regions controlling cell identity genes highlight the key TFs of each major cell type. The gene regulatory differences between the mouse strains manifest more on transcriptome than chromatin level.