MERFISH spatial transcriptomics dataset of a single adult mouse brain

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-638850/20241115	1.81 GB

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

Related resources :

Imputed, whole mouse brain MERFISH spatial transcriptomics dataset (MERFISH-C57BL6J-638850-imputed)
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.
- MERFISH imputed genes: Learn about the using the imputed genes of the MERFISH dataset.