Spatial transcriptomics allows for high-resolution genome-wide detection of transcripts and their spatial location, which in contrast to single cell or single nuclei transcriptomics makes it possible to investigate all cells including rare cells in a single tissue section while maintaining information on the cellular environment and neighboring cells. In the Brain resource there is spatial transcriptomics data of the human ‘healthy’ cerebral cortex (frontal cortex) with information on protein-coding transcripts in the five main cell-types of the human cerebral cortex. Based on single nuclei transcriptomics and spatial transcriptomics data the location of vascular cells, astrocytes, oligodendrocytes, microglia and neurons was determined using sets of marker genes with elevated expression in the corresponding cell-types so that every location within the spatial transcriptomics data can be linked to a main cell type. The data was also used to the get the number of counts for each protein-coding transcript in each of the cell types.

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Key publications

• Ståhl PL et al., Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. (2016)
  PubMed: 27365449 DOI: 10.1126/science.aaf2403

• Chen A et al., Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell. (2022)
  PubMed: 35512705 DOI: 10.1016/j.cell.2022.04.003

• Liu L et al., Spatiotemporal omics for biology and medicine. Cell. (2024)
  PubMed: 39178830 DOI: 10.1016/j.cell.2024.07.040