Whole mouse brain 10Xv3 single cell transcriptomes#

This dataset consists of 2.3 million single cell transcriptomes spanning the whole adult mouse brain using 10Xv3 chemistry.

It was used in the creation of a high resolution transcriptomic and spatial atlas of cell types described in Yao et al..

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


Current Version


Expression Matrices


176.31 GB

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

Related resources :

  • Whole mouse brain clustering (WMB-10X)

  • Whole mouse brain mouse taxonomy of cell types (WMB-taxonomy)

Associated notebooks:

  • Getting started: learn how to use the AbcPorjectCache 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.