Whole adult mouse brain taxonomy of cell types#

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. The combination of scRNA-seq and MERFISH data reveals a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type, as well as unique features of cell type organization in different brain regions.

A detailed cell type annotation table is also provided along with data downloads detailing information about the hierarchical membership, anatomical annotation, neurotransmitter type, cell type marker genes, transcription factor and neuropeptide markers, and other metadata types for each cluster.

The associated metadata is hosted on AWS S3 bucket as a AWS Public Dataset:

Component

Current Version

Size

Metadata

s3://allen-brain-cell-atlas/metadata/WMB-taxonomy/20231215

0.01 GB

Data is being share under the CC BY NC 4.0 license.

Related resources :

Associated notebooks:

  • Getting started: learn how to use the AbcProjectCache to facilitate data download and usage.

  • 10x scRNA-seq clustering analysis and annotation: learn about the whole mouse brain taxonomy through some example use cases and visualization.

  • 10x scRNA-seq gene expression data

    • Part 1: learn about the 10x dataset through some example use cases and visualization of cells in the thalamus.

    • Part 2a: learn how to iterate through all the data packages, to access data for whole brain example use cases in part 2b.

    • Part 2b: Explore the whole brain data through visualization and analyses of a set of genes of interest.

  • MERFISH whole brain spatial transcriptomics

    • Part 1: learn about the MERFISH dataset through some example use cases and visualization for a single brain section.

    • Part 2a: learn to access data and prepare for whole brain example use cases in part 2b.

    • Part 2b: Explore the whole brain data through visualization and analyses of a set of genes of interest.