<b>Comprehensive Single-Cell Transcriptomic Atlas of the Mouse Pons and Medulla</b>

This integrated dataset represents the large-scale transcriptomics cell atlas of pons and medulla, compiled from 8 independent single-cell/single-nucleus RNA sequencing (sc/sn-RNA seq) datasets. This integration was performed using a standardized bioinformatic workflow, clustering, and marker-based annotation. This dataset comprised 317 985 quality-passed cells with 45 cell types.This dataset offers a valuable source for single-cell neuroscience to understand region-specific molecular insights and their cellular diversity.To aid interpretability, annotations are structured hierarchically into three levels:<b>Level 1</b>: Broad categories (e.g., Neurons, Astrocytes, Oligodendrocytes)<b>Level 2</b>: Subtypes within broad categories (e.g., Excitatory neurons, Inhibitory neurons)<b>Level 3</b>: Fine-grained subtypes (e.g., Glut1, Glut2, GABA1, GABA2).In addition, we also incorporated label transfer from the <b>Yao et al. (</b>https://doi.org/10.1038/s41586-023-06812-z<b>)</b> to benchmark and validate our annotations. Transferred Yao labels are included in the metadata as <code>predicted.Class</code>, <code>predicted.Subclass</code>, and <code>predicted.Neurotransmitter</code>, together with associated confidence scores.We provide the following datasets to facilitate reuse:<b>Final_Integrated_Pons_Medulla.rds</b>Contains all neuronal and non-neuronal populations.The <code>cell_type</code> column includes Level 1, Level 2, and Level 3 annotations combined.<b>Pons_Medulla_Neurons_level_3.rds</b>Subset of neuronal populations.Includes <b>Level 2 and Level 3 annotations</b> for neurons in the <code>cell_type</code> column.<b>GABA_Gluta.rds</b>Subset of <b>excitatory (glutamatergic)</b> and <b>inhibitory (GABAergic)</b> neuronal populations.Includes <b>Level 3 annotations</b> for detailed analysis of these key neurotransmitter systems.<br>