Single-nucleus multiple-organ chromatin accessibility mapping in the rat

Summary The chromatin accessibility landscape is the basis of cell-specific gene expression. We generated a multiorgan, 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), the dynamics of T-cell developmental trajectories across organs, and the conservation and specificity of gene expression patterns across species. These findings provide a foundation for further investigations of the cell composition and gene regulatory networks throughout the rat body. Highlights Generation of a single-cell atlas of chromatin accessibility in nine organs of the rat Characterization of cell type- and organ-specific transcription factors (TFs) Dynamics of chromatin accessibility in developing T cells revealed by cross-organ analysis Conservation and specificity of gene expression patterns among humans, mice, and rats revealed by cross-species analysis