Spatial Omics Solutions for Astrocytes

Spatial Omics Solutions for Astrocytes

Astrocytes are the major component of glial cells in the nervous system. As the most abundant class of cells in the brain, astrocytes play an important physiological function in maintaining the homeostasis of the brain microenvironment. Astrocytes can express immune mucosal molecules, secrete inflammatory factors and release complement, etc., which are involved in the development of inflammatory diseases in the brain and play an important role in neuroimmune function. However, experimental tools that allow detailed astrocyte characterization is lacking, so the issue of their diversity and heterogeneity remains to be addressed.

Reactive astrogliosis in two degenerative diseases.Figure 1. Reactive astrogliosis in two degenerative diseases. (Sofroniew, M. V., et al., 2010)

How we use spatial omics to dissect astrocytes

CD Genomics comprehensively phenotypes astrocytes at single-cell resolution while maintaining spatial relationships with neuropathic lesion cells, and after integrating highly multiplexed imaging into the spatial information, allows our clients to further elucidate astrocyte heterogeneity. In addition to this, we use highly multiplexed imaging in combination with computational analysis processes to provide insight into the functional state and spatial organization of astrocytes in lesions.

Our clients can get

  • Identify astrocyte subtypes using scRNA-seq and single-cell spatial transcriptomics to distinguish different astrocyte subtypes using Smart-seq2.
  • Reveal the different spatial localization of defined subtypes by in situ validation to understand the distribution of morphologically and physiologically distinct astrocyte populations.
  • Allows the combination of super-resolution microscopy with FISH, enabling multiplexing of over 20,000 genes in a single cell with high precision and subdiffraction-limited resolution.
  • The source of variation in marker expression is quantified by spatial variance component analysis (SVCA) using marker mapping and spatial coordinates for each cell.
  • SmFISH is used to define different regions of astrocyte subpopulations and map snRNA-seq-derived phenotypes to diseased tissue.

Sample(s) available for analysis: FFPE tissue section

Practical applications

  • Localize cell subpopulations in a tissue environment.
  • Quantify single-cell RNA levels in a spatial environment.
  • Identify phenotypic localization and cell-to-cell interactions in a given microenvironment.
  • Identify spatial interactions and phenotypic transition trajectories in a spatial environment.
  • Annotate functional (receptor-ligand) cellular interactions and pathways.

We do it better

CD Genomics offers spatial omics combined with a highly multiplexed and computerized analysis process that allows our clients to annotate constituent subpopulations of astrocytes and cellular interactions during key pathological processes, as well as precisely outline astrocytes with complex, irregular morphologies. This will help address the diverse, heterogeneous nature of astrocytes to identify new therapeutic targets to improve disease progression and promote neural repair.


  1. Sofroniew, M. V., et al., (2010). "Astrocytes: biology and pathology." Acta neuropathologica, 119(1), 7-35.
For research use only, not intended for any clinical use.

Online Inquiry