Human brain 10Xv3 single nucleus transcriptomes#

This dataset consists of nuclei extracted from over three million single cells (approximately two million neurons and one million non-neurons) from 100 locations across the forebrain, midbrain, and hindbrain.

Full details on the dataset can be found in Siletti et al. 2023.

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


Current Version


Expression Matrices


70.0 GB

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

Related resources:

  • Clustering analysis of over 3 million single nucleus transcriptomes spanning the whole adult human brain (WHB-10X-clustering)

  • Whole human brain taxonomy of cell types (WHB-taxonomy)

Associated notebooks:

  • Getting started: learn how to use the manifest.json file to facilitate data download and usage.

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

  • Accessing 10X gene expression data: learn how to load individual genes from the 10X expression data.

  • 10x scRNA-seq gene expression data

    • Part 1: understand the basic structure of the data and metadata, and visualize brain region and cell type annotations in a UMAP.

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