Spatial atlas of the mouse central nervous system at molecular resolution.

ABSTRACT: Spatially charting molecular cell types at single-cell resolution across the 3D volume is critical for illustrating the molecular basis of brain anatomy and functions. Single-cell RNA sequencing has profiled molecular cell types in the mouse brain^1,2, but cannot capture their spatial organization. Here we used an in situ sequencing method, STARmap PLUS^3,4, to profile 1,022 genes in 3D at a voxel size of 194 × 194 × 345 nm³, mapping 1.09 million high-quality cells across the adult mouse brain and spinal cord. We developed computational pipelines to segment, cluster and annotate 230 molecular cell types by single-cell gene expression and 106 molecular tissue regions by spatial niche gene expression. Joint analysis of molecular cell types and molecular tissue

SUBMITTER: Shi H 

PROVIDER: S-EPMC10709140 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature