Molecular atlas of the adult mouse brain.
Dataset ID: STDS0000066
34,103 Spots
23,371 Genes


Dataset information
Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain organization based on unbiased extraction of spatially-defining features. Applying whole-brain spatial transcriptomics, we captured the gene expression signatures to define the spatial organization of molecularly discrete subregions. 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. In summary, we have established a new molecular atlas to formally define the identity of brain regions, and a molecular code for mapping and targeting of discrete neuroanatomical domains.
Overall design
We hybridized 75 coronal sections from one brain hemisphere of 3 adult mice with Spatial Transcriptomics and defined a molecular atlas using clustering algorithms.
Spatial Transcriptomics
Illumina NextSeq 500
Mus musculus
Development stage
9 weeks
Ortiz C, Navarro JF, Jurek A, Märtin A et al. Molecular atlas of the adult mouse brain. Sci Adv 2020 Jun;6(26):eabb3446.
Submission date: 2020-03-30Update date: 2020-07-13
Sample number: 75

Cantin Ortiz; Jose Fernandez Navarro; Aleksandra Jurek; Antje Märtin; Joakim Lundeberg; Konstantinos Meletis

GEO Series Accessions: GSE147747