Spatial transcriptomics map of the embryonic mouse brain – a tool to explore neurogenesis
Dataset ID: STDS0000235
19,968 Spots
32,285 Genes


Dataset information
The developing brain has a complex and well-organized anatomical structure comprising different types of neural and non-neural cells. Stem cells, progenitors, and newborn neurons tightly interact with their neighbouring cells and tissue microenvironment, and this intricate interplay ultimately shapes the output of neurogenesis. Given the relevance of spatial cues during brain development, we acknowledge the necessity for a transcriptomics atlas within the tissue context accessible to the neurodevelopmental community. To fulfil this need, we offer an open-access spatial gene expression browser of the embryonic mouse brain at the peak of neurogenesis. Using 10x Visium technology, we generated spatially-resolved RNAseq data from E13.5 embryonic brain sections. Unsupervised clustering reliably defined specific cell type populations of diverse lineages and maturational states. Differential expression analysis revealed unique transcriptional signatures across specific embryonic brain areas, uncovering novel features inherent to particular anatomical domains. Furthermore, we integrated single-cell RNAseq data from E13.5 mouse brains into our Spatial Transcriptomics data, adding tissue context to single-cell resolution. In summary, we provide a valuable tool that enables the exploration and discovery of unforeseen molecular players involved in neurogenesis, particularly in the crosstalk between different cell types.
Overall design:
Four sections from four different WT mouse embryonic heads (stage E13.5) were extracted for spatial transcriptomics using the 10x Genomics Visium platform in order to identify areas of the embryonic brain with different cell lineages and maturation states at the peak of neurogenesis.
10x Visium
Mus musculus(mm10)
Development stage:
F | M
Di Marco, Barbara et al. “Spatial transcriptomics map of the embryonic mouse brain - a tool to explore neurogenesis.” Biology open vol. 12,10 (2023): bio060151. doi:10.1242/bio.060151
Submission date: 2023-08-11Update date: 2023-10-13
Sample number: 4Section number: 4

Di Marco B, Vázquez-Marín J, Monyer H, Centanin L, Alfonso J

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