Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat

The chromatin accessibility landscape is the basis of cell-specific gene expression. We generated a multi organ, single-nucleus chromatin accessibility landscape from the model organism Rattus norvegicus. For this single-cell atlas, we constructed 25 libraries via snATAC-seq from nine organs in the rat, with a total of over 110,000 cells. Cell classification integrating gene activity scores with known marker genes identified 77 cell types, which were strongly correlated with those in published mouse single-cell transcriptome atlases. We further investigated the enrichment of cell type- and organ-specific transcription factors (TFs), Shared and organ-specific features of endothelial and stromal cells, and the conservation and specificity of gene regulatory programs across species. Together, these findings provide a valuable foundation for dissecting tissue-specific regulatory logic and for advancing cross-organ and cross-species cell type annotation and functional inference in the rat model.