This dataset consists of 1.7 million single cell transcriptomes spanning the whole adult mouse brain using 10Xv2 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:
| Component | Current Version | Size |
|---|---|---|
| Expression Matrices | s3://allen-brain-cell-atlas/expression_matrices/WMB-10Xv2/20230630 | 104.05 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.