Comprehensive Single-Cell Transcriptomic Atlas of the Mouse Pons and Medulla

The pons and medulla, key regions of the hindbrain within the brainstem, regulate a wide range of complex behaviors, ranging from motor control to autonomic regulation and reflexes. As the central hub of neural projections and gut-to-brain communication, the cellular diversity that supports these functions remains ambiguous. To address this, we integrated eight single-cell and single-nucleus RNA sequencing (sc/snRNA-seq) datasets from mouse brains. We constructed a large-scale single-cell atlas encompassing 318,522 single cells from different sub-regions of the pons and medulla. Using a rigorous metadata standardization and annotation approach, we identified 45 cell types that span major populations and exhibit subtype-specific variability. We observed high diversity among neuronal populations, while non-neuronal cells were dominated by glial and vascular cells, each with unique transcriptional profiles. This atlas serves as the foundational resource for exploring region-specific cellular diversity in the pons and medulla, enabling comparative analyses for future studies.