Allen Brain Mouse Whole-Brain Transcriptomic Cell Type Atlas
The Mouse Whole Brain Atlas is a high-resolution transcriptomic and spatial cell-type atlas across the entire mouse brain, integrating several whole-brain single-cell RNA-sequencing (scRNA-seq) datasets. The datasets contain a total of ~4 million cells passing rigorous quality-control (QC) criteria. The integrated transcriptomic taxonomy contains 5,322 clusters that are organized in a hierarchical manner with nested groupings of 34 classes, 338 subclasses, 1,201 supertypes and 5,322 types/clusters. The scRNA-seq data reveal transcriptome-wide gene expression and co-expression patterns for each cell type. The anatomical location of each cell type has been annotated using a comprehensive brain-wide MERFISH dataset with a total of ~4 million segmented and QC-passed cells, probed with a 500-gene panel and registered to the Allen Mouse Brain Common Coordinate Framework (CCF v3). The MERFISH data not only provide accurate spatial annotation of cell types at subclass, supertype and cluster levels, but also reveal fine-resolution spatial distinctions or gradients for cell types.
Platform: MERSCOPE4.0M cells/molecules550 genes