Fig. 3. In situ major cell type tropism profiling of barcoded systemic AAV capsid pools in mouse cortex.

a, Experimental pipeline. We designed a pool of six AAV capsid variants carrying unique barcodes and administered them to adult wild-type mice through retro-orbital injection. At 4 weeks after injection, we harvested the brain tissue and used USeqFISH to profile viral gene expression along with endogenous cell type marker genes. The image dataset was then converted to a gene-by-cell expression matrix via our automated image processing pipeline, and we quantitatively analyzed the data by clustering endogenous genes to identify cell type clusters, followed by viral gene expression profiling in each cluster. b, Representative image of six variants and ten cell type markers in the same region of the mouse cortex. c, Transduction efficiency, measured by % transduced cells, of each variant in two mice (mean ± s.e.m.; n = 5 for mouse 1; n = 6 for mouse 2). d, Endogenous (top, cividis color map) and viral gene expression profiles (enrichment: middle, viridis; relative tropism bias: bottom, coolwarm) in the cell type clusters.