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 describe in Yao et. al.
The expression matrices and associated metadata is hosted on AWS S3 bucket as a AWS Public Dataset:
Data is being share under the CC BY NC 4.0 license.
Related resources :
Whole mouse brain mouse brain clustering (WMB-10X)
Whole mouse brain mouse taxonomy of cell types (WMB-taxonomy)
Getting started: learn how to use the manifest.json file to faciliate 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.