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

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:Level 1: Broad categories (e.g., Neurons, Astrocytes, Oligodendrocytes)Level 2: Subtypes within broad categories (e.g., Excitatory neurons, Inhibitory neurons)Level 3: Fine-grained subtypes (e.g., Glut1, Glut2, GABA1, GABA2).In addition, we also incorporated label transfer from the Yao et al. (https://doi.org/10.1038/s41586-023-06812-z) to benchmark and validate our annotations. Transferred Yao labels are included in the metadata as predicted.Class, predicted.Subclass, and predicted.Neurotransmitter, together with associated confidence scores.We provide the following datasets to facilitate reuse:Final_Integrated_Pons_Medulla.rdsContains all neuronal and non-neuronal populations.The cell_type column includes Level 1, Level 2, and Level 3 annotations combined.Pons_Medulla_Neurons_level_3.rdsSubset of neuronal populations.Includes Level 2 and Level 3 annotations for neurons in the cell_type column.GABA_Gluta.rdsSubset of excitatory (glutamatergic) and inhibitory (GABAergic) neuronal populations.Includes Level 3 annotations for detailed analysis of these key neurotransmitter systems.