Consensus Whole Mouse Brain single cell/nucleus transcriptomes#

Expression matrices and metadata for the two combined whole mouse brain datasets, Allen Institute for Brain Science (AIBS), Whole Mouse Brain (WMB) and a release from the Broad Institute, Macosko lab. The previously, released WMB-AIBS, dataset released through this tool contains over 4 million scRNA-seq profiles. The additional whole mouse brain data from Broad Institute data (referred to here as WMB-Macosko) contains and additional 4 million snRNA-seq profiles. These two scRNA-seq and snRNA-seq datasets (WMB and Macosko respectively) are combined here into this Consensus Mouse release and Consensus Mouse Taxonomy.

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

Below are links to the data and metadata from the WMB-Macosko whole mouse brain, snRNA-seq data.

Component

Current Version

Size

Macosko: Expression Matrices

s3://allen-brain-cell-atlas/expression_matrices/Consensus-WMB-Macosko-10X/20251031/

42.7 GB

Macosko: Cell and gene metadata

s3://allen-brain-cell-atlas/metadata/Consensus-WMB-Macosko-10X/20251031/

798.3 MB

This release re-uses the AIBS WMB scRNA-seq dataset expression matrices, specifically the WMB-10Xv2 and WMB-10Xv3 data. We do release a set of updated metadata that contain the cells which pass the Consensus WMB taxonomy QC. Consensus Mouse Taxonomy. The set of cells in this metadata are largely the same set of cells as those listed in the WMB-10X metadata, differing only by roughly a few thousand.

Component

Current Version

Size

AIBS: Cell and gene metadata

s3://allen-brain-cell-atlas/metadata/Consensus-WMB-AIBS-10X/20251031/

634.9 MB

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

Related resources:

Associated notebooks: