Clustering analysis of 4.0 million single cell transcriptomes spanning the whole adult mouse brain combining the 10Xv2 and 10Xv3 datasets, resulting in a set of 5196 clusters.
This is one of the steps towards creating a high resolution transcriptomic and spatial atlas of cell types described in Yao et al..
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-10X/20241115 | 2.39 GB |
Data is being share under the CC BY NC 4.0 license.
Related resources :
- Whole mouse brain 10Xv2 single cell transcriptomes (WMB-10Xv2)
- Whole mouse brain 10Xv3 single cell transcriptomes (WMB-10Xv3)
- Whole mouse brain 10XMulti single cell transcriptomes (WMB-10XMulti)
- Whole mouse brain mouse taxonomy of cell types (WMB-taxonomy)
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.