Welcome to Brain Spatial Atlas Portal!

Checkout our paper: Spatial atlas of the mouse central nervous system at molecular resolution!

This site presents a spatial molecular atlas of the adult mouse central nervous system (CNS) generated by Xiao Wang’s lab with STARmap and STARmap PLUS, an imaging-based targeted in situ sequencing platform, and ClusterMap, an unsupervised and annotation-free framework for cell and tissue segmentation.

This dataset contains spatial gene expression profiles of 1,022 genes mapped in 3D at a voxel size of 194 X 194 X 345 nm³ in 1.09 million high-quality cells in the mouse CNS. We annotated (230 molecular cell types) by single-cell gene expression and (106 molecular tissue regions) by spatial niche gene expression. We also integrated STARmap PLUS measurements with a published scRNA-seq atlas, imputing single-cell expression profiles of 11,844 genes. Finally, we delineated viral tropisms of a brain-wide transgene delivery tool, AAV-PHP.eB.

You can explore the data using the following links or tabs on navigation bar:

Spatial-Portal of adult mouse CNS:

• Spatial gene expression of 1,022 cellular genes and AAV-PHP.eB expression;
• Spatial distribution of molecular cell type annotation (26 main types, 230 subtypes);
• Spatial distribution of molecular tissue regions (106 regions).

Averaged gene expression in each molecular cell types and tissue regions can be downloaded here (molecular cell type, molecular tissue region).

To download the data, please visit our depositions at the Single Cell Portal and Zenodo.

• Subcellular reads information in identified cells in individual tissue slices (sample_spot_meta.csv);
• Raw in situ sequencing read count in single cells in individual tissue slices (sample_raw_expression_pd.csv);
• Processed single-cell gene expression in individual tissue slices after normalization and across-slice batch correction (sample_processed_expression_pd.csv);
• Spatial coordinates and annotations for identified cells in individual tissue slices (sample_spatial.csv);
• Imputed single-cell gene expression of 11,844 genes in individual tissue slices (imputation_sample.h5ad).

The code that supports the analyses in this study is available at https://github.com/wanglab-broad/mCNS-atlas.

Please email xwangx@mit.edu or wangxiao@broadinstitute.org with any questions, comments, or queries.

This site is managed by the Wang lab at the Broad Institute.