A Molecular Atlas of the Adult Mouse Brain

We applied whole-brain Spatial Transcriptomics on mice to define the spatial organization of molecularly discrete subregions by capturing the gene expression signatures. We found that the molecular code contained sufficiently detailed information to directly deduce the complex spatial organization of the brain. This unsupervised molecular classification revealed new area and layer-specific subregions, for example in isocortex and hippocampus, and a new division of striatum. The whole-brain molecular atlas further supports the identification of the spatial origin of single neurons using their gene expression profile, and forms the foundation to define a minimal gene set - a brain palette - that is sufficient to spatially annotate the adult brain.

This video summarizes the methods we applied in order to establish a brain atlas based solely on the molecular signature.

This videos shows several subdivisions of the isocortex.

This videos shows several subdivisions of the striatum.

We developed an online interactive viewer to visualize the atlas and the gene expression patterns both in 2D and 3D, using the Plotly library.

info iconPlease note that the viewer will load about 100MB using your internet connection.

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This work was published in Science Advances, a peer-reviewed journal.

Citation: C. Ortiz*, J. F. Navarro*, A. Jurek, A. Märtin, J. Lundeberg, K. Meletis, Molecular atlas of the adult mouse brain. Sci. Adv. 6, eabb3446 (2020).

We made the data gathered during this project entirely open source. You are very welcome to use the dataset for your own research and we would be happy to answer any of your questions. If you appreciate our efforts, please don’t forget to cite our work as this will allow us to keep sharing more and more data in the future.

Although we recommend the online viewer for its easy-of-use, speed and compatibility, we have upgraded a previously published tool to support 3D datasets as well as 2D datasets. The new ST Viewer is cross-platform, it does not require internet connection and it provides some additional functionalities that may be of interest.

  • Visualization of genes and/or clusters.
  • Visualization of multiple genes at a time.
  • Visualization of genes at specific clusters.
  • Possibility to select spots/clusters and use them for downstream analysis.
  • Possibility to upload custom clustering results.
  • Enhanced visualization options (thresholds, normalization, visualization modes etc.)
  • Integrated analysis tools.

The necessary data files to use the ST Viewer are provided in the download section of the website.

All the code used for this study is available on GitHub. You are welcome to reuse it as long as you provide proper reference.

Reference: Ortiz et al., Molecular atlas of the adult mouse brain. Sci. Adv. 6, eabb3446 (2020)
Website contact: Cantin Ortiz