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 describe in Yao et. al.

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

Component

Current Version

Size

Expression Matrices

s3://allen-brain-cell-atlas/expression_matrices/WMB-10Xv3/20230630

176.31 GB

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

Related resources :

  • Whole mouse brain mouse brain clustering (WMB-10X)

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

Associated notebooks:

  • Getting started: learn how to use the manifest.json file to faciliate 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.