< No: 40
2024


Spatial transcriptomics

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


Human cortex 5 cell-types spatial transcriptomics

Figure legend: Assignment of spots to the 5 main cell-types. The colors represent the masks for the main cell types. These are used to assign pixels to cell types when counting transcripts or imputing expression.


Key facts

  • 15895 proteins has spatial transcriptomics data for cerebral cortex