# 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](https://www.science.org/doi/10.1126/science.add7046).

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

| Component | Current Version | Size    |
|---|--|---------|
| Expression Matrices | [s3://allen-brain-cell-atlas/expression_matrices/WHB-10Xv3/20240330/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#expression_matrices/WHB-10Xv3/20240330/) | 70.0 GB |
| Cell and gene metadata | [s3://allen-brain-cell-atlas/metadata/WHB-10Xv3/20241115](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#metadata/WHB-10Xv3/20241115/) | 862.1 MB |
| MapMyCells resources | [s3://allen-brain-cell-atlas/mapmycells/WHB-10Xv3/20240831/](https://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/index.html#mapmycells/WHB-10Xv3/20240831/) | 8.1 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](WHB-10X-clustering.md))
* Whole human brain taxonomy of cell types ([WHB-taxonomy](WHB-taxonomy.md))

Associated notebooks:
* [**Getting started**](../notebooks/getting_started.ipynb): learn how to use the manifest.json file to
  facilitate data download and usage.
* [**10x scRNA-seq clustering analysis and annotation**](../notebooks/WHB_cluster_annotation_tutorial.ipynb):
  learn about the whole human brain taxonomy through some example use cases and
  visualization.
* [**Accessing 10X gene expression data**](../notebooks/general_accessing_10x_snRNASeq_tutorial.ipynb):
  learn how to load individual genes from the 10X expression data.
* **10x scRNA-seq gene expression data**
  * [**Part 1**](../notebooks/WHB-10x_snRNASeq_tutorial_part_1.ipynb): understand the basic structure of the data and metadata,
    and visualize brain region and cell type annotations in a UMAP.
  * [**Part 2**](../notebooks/WHB-10x_snRNASeq_tutorial_part_2.ipynb): explore the whole brain data through visualization and
    analyses of a set of genes of interest.