Single-cell spatial transcriptomic atlas of the whole mouse brain.

Area of Science:

• Neuroscience
• Genomics
• Spatial Transcriptomics

Background:

• Understanding mammalian brain function requires a detailed map of cell types and gene expression.
• Existing atlases often lack single-cell resolution or comprehensive spatial information.

Purpose of the Study:

• To create a high-resolution spatial transcriptomic atlas of the entire mouse brain.
• To identify cell clusters, gene expression patterns, and their relationship to brain structure and disease.

Main Methods:

• Single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq were employed.
• Analysis covered over 4 million cells and 29,655 genes at single-cell resolution.

Main Results:

• Generated a mouse brain atlas with 308 distinct cell clusters and genome-wide gene coverage.
• Identified region-specific cell clusters, 155 brainstem-enriched genes, and 513 region-enriched long non-coding RNAs.
• Uncovered 411 transcription factor regulons with spatiotemporal dynamics during neurodevelopment.

Conclusions:

• The developed atlas provides unprecedented spatial and single-cell resolution of the mouse brain.
• This resource facilitates research into brain function, development, and disease mechanisms.