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Getting Started

Welcome to BrainCellData!

This site is managed by the Macosko lab at the Broad Institute to accompany our recent manuscript - The molecular cytoarchitecture of the adult mouse brain as part of the BICCN 2.0 Initiative.

It is home to two comprehensive brain-wide datasets datasets:

  1. A snRNA-seq (single-nuclei RNA-sequencing) atlas of 4,998 transcriptionally defined cell type clusters
  2. A Slide-seq spatial spatial transcriptomics atlas of one mouse brain hemisphere, generated together with Fei Chen’s lab.

For downloading the data, go to the Downloads tab.

For exploring the data in the viewer, go to the Viewer application.

Information about the Viewer components, functionality, and architecture can be found in the following pages (navigate using navigation bar or use the links that appear below on this page).

Viewer Overview

The Brain Cell Data viewer is a web application that allows users to view and explore brain cell data. It is composed of three, interlinked tabs:

  • GeneExp allows users to plot the expression of one or two genes in the Slide-seq atlas.

  • SingleCell helps to identify clusters by gene-expression and gives searchable accompanying metadata.

  • CellSpatial shows the spatial localization of the snRNA-seq cell types in the Slide-seq dataset.

For detailed information about each tab of the viewer, see the respective viewer subsections in the documentation.