MERFISH spatial transcriptomics dataset of a single adult mouse brain

A 4.0 million cell spatial transcriptomics dataset spanning a single adult mouse brain with a 500 gene panel and mapped to the whole mouse brain taxonomy. 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/MERFISH-C57BL6J-638850/20230830	14.2 GB
Metadata	s3://allen-brain-cell-atlas/metadata/MERFISH-C57BL6J-638850/20231215	1.81 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 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.

• • MERFISH whole brain spatial transcriptomics

  • Part 1: learn about the MERFISH dataset through some example use cases and visualization for a single brain section.

  • Part 2a: learn to access data and prepare 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.