In a publication in the journal Neuron a group of scientists including Jan Mulder, an HPA-related researcher, have used Stereo-seq, in combination with single-nucleus RNA sequencing data to create a 3-D atlas showing the cell-type distribution across the whole mouse brain. The spatial distributions of diverse cell types and lncRNAs in adult brain as well as the spatiotemporal profile of gene expression during brain development were investigated.

The mouse is the most widely used animal model and to better understand the mouse brain, this complex organ with diverse cell types having specific distribution and connectivity, an atlas with genome-wide single-cell and high spatial resolution data could be an important contribution. In this study Stereo-seq, a spatial transcriptomic technology with single-cell resolution combined with single-nucleus RNA sequencing was used to create such a map of the whole adult mouse brain.

Findings included the discovery of more than 400 transcription factor regulons displaying regional selectivity during neurodevelopment and that almost 10% of mouse brain lncRNA display regional enrichment according to spatial distribution analysis.Further the relationship between cell types and neurological diseases was investigated using enrichment analysis across cell subclasses and clusters, which revealed differences in proportions of two dopaminergic clusters in the substantia nigra in relation to Parkinson's disease.

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