Fig. 1: In vivo spatial perturb-seq of the adult mouse brain by intracranial injection of a barcoded AAV library.

a Schematic of the in vivo spatial Perturb-seq pipeline, and depiction of components in our AAV-PHP.eB library, showing 3 gRNAs, TdTomato and 1 barcode in each member. Created in BioRender. Shen, K. (2026) https://BioRender.com/1ox9bo3. b Confocal imaging of a coronal section of a mouse brain following stereotaxic injection into the hippocampus, showing that transduction spread is limited to the hippocampus region. Scale bar: 1000 µm. n = 5 mice. c UMAP projection of cells from chip 1 following Stereo-seq, showing recovery of neurons, oligodendrocytes, choroid plexus cells, RBCs, microglia, endothelial cells, and astrocytes. Left: coloured by cluster number. Right: coloured by cell type. d Similar proportions of cell types were recovered for each chip, with the majority cell type being neurons as expected. e Dot Plot showing expression of cell-type enriched genes for each cell type. f Spatial scatter of annotated mouse brain cells. g Spatial gene plot of canonical cell-type markers major cell populations (Microglia: C1qa; Oligodendrocytes: Mbp; Endothelial cells: Flt1; Neurons: Snap25; Astrocytes: Gfap, Choroid Plexus: Ttr; RBC: Hba-a1; Immature oligodendrocytes: Birc5). h ssDNA image for cellular localization on the Stereo-seq chip. i Spatial scatter following BANKSY clustering with lamba 0.2, showing clusters recovered. j Selection of CA and DG neurons in the hippocampus by focusing on BANKSY clusters 3 and 10. k Subset of barcode-positive cells from (j). l Piechart representation of the number of unique gRNA barcodes among all gRNA barcode positive cells, showing a small proportion of barcode-positive cells with multiple barcodes detected. m Dot Plot showing percentage of barcode-positive neurons among hippocampal neurons in (j) for each chip. n Total number of cells for each gRNA across all 3 chips. Min: 29, max: 330, mean: 122. f–l Data from chip 1.